Query 030201
Match_columns 181
No_of_seqs 151 out of 848
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 10:05:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030201.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030201hhsearch_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 1.1E-47 2.3E-52 291.5 12.0 180 1-180 1-181 (181)
2 PRK14560 putative RNA-binding 100.0 1.6E-42 3.6E-47 268.9 18.7 158 9-178 2-159 (160)
3 COG2016 Predicted RNA-binding 100.0 3.5E-42 7.5E-47 263.1 16.4 159 9-179 2-160 (161)
4 TIGR03684 arCOG00985 arCOG0415 100.0 1.3E-40 2.8E-45 255.7 18.9 149 14-176 2-150 (150)
5 KOG2522 Filamentous baseplate 100.0 8.8E-37 1.9E-41 262.4 14.1 173 1-180 1-178 (560)
6 TIGR00451 unchar_dom_2 unchara 100.0 2.2E-29 4.9E-34 183.1 11.9 107 61-172 1-107 (107)
7 PRK13534 7-cyano-7-deazaguanin 99.9 2.9E-23 6.3E-28 190.1 15.7 150 15-171 484-638 (639)
8 PRK13795 hypothetical protein; 99.9 2.5E-21 5.4E-26 178.1 15.7 146 14-171 46-201 (636)
9 PRK13794 hypothetical protein; 99.8 2.8E-20 6E-25 166.2 15.4 145 15-170 45-199 (479)
10 COG1370 Prefoldin, molecular c 99.8 9.6E-20 2.1E-24 137.2 13.1 146 15-168 2-152 (155)
11 PF01472 PUA: PUA domain; Int 99.8 3.1E-19 6.7E-24 121.6 6.5 74 92-170 1-74 (74)
12 TIGR00432 arcsn_tRNA_tgt tRNA- 99.8 2.3E-18 5.1E-23 155.1 13.9 145 16-167 388-537 (540)
13 COG5270 PUA domain (predicted 99.6 9.7E-15 2.1E-19 113.7 11.4 141 15-167 49-199 (202)
14 smart00359 PUA Putative RNA-bi 99.3 2.8E-11 6.1E-16 82.0 7.9 74 93-171 2-77 (77)
15 TIGR00425 CBF5 rRNA pseudourid 99.2 7.6E-11 1.7E-15 100.8 9.2 78 91-173 237-314 (322)
16 PRK04270 H/ACA RNA-protein com 99.1 3E-10 6.6E-15 96.3 8.9 76 91-171 225-300 (300)
17 PRK05429 gamma-glutamyl kinase 99.0 2.3E-09 4.9E-14 93.5 8.6 64 89-157 278-342 (372)
18 COG1549 Queuine tRNA-ribosyltr 98.9 7.1E-09 1.5E-13 91.9 10.1 69 91-170 450-518 (519)
19 TIGR01027 proB glutamate 5-kin 98.7 5.9E-08 1.3E-12 84.4 8.3 63 90-157 271-334 (363)
20 PF09183 DUF1947: Domain of un 98.5 5.3E-07 1.2E-11 59.3 6.3 63 13-87 2-64 (65)
21 PRK08557 hypothetical protein; 98.3 2.3E-06 5E-11 75.7 8.5 127 15-162 8-141 (417)
22 PRK13402 gamma-glutamyl kinase 98.0 2E-05 4.4E-10 68.7 7.4 63 90-157 275-338 (368)
23 PF14810 TGT_C2: Patch-forming 97.9 2.2E-05 4.8E-10 53.3 4.2 61 22-84 2-63 (74)
24 COG0263 ProB Glutamate 5-kinas 97.4 0.00036 7.8E-09 60.2 6.0 61 91-157 279-340 (369)
25 PRK14124 tRNA pseudouridine sy 96.2 0.018 4E-07 49.2 7.0 74 91-170 228-305 (308)
26 KOG2529 Pseudouridine synthase 95.8 0.005 1.1E-07 53.9 2.0 77 91-172 275-351 (395)
27 KOG3492 Ribosome biogenesis pr 92.3 1.6 3.5E-05 33.7 8.7 143 15-170 3-167 (180)
28 PF03657 UPF0113: Uncharacteri 90.2 0.56 1.2E-05 36.5 4.6 119 15-148 5-141 (162)
29 PRK00130 truB tRNA pseudouridi 87.5 1.5 3.3E-05 37.2 5.7 50 91-148 229-278 (290)
30 PF09157 TruB-C_2: Pseudouridi 86.1 2.7 6E-05 26.4 5.1 47 92-149 1-47 (58)
31 PRK05033 truB tRNA pseudouridi 81.3 3.9 8.5E-05 35.1 5.5 47 91-148 249-295 (312)
32 COG0130 TruB Pseudouridine syn 80.7 2.7 5.8E-05 35.4 4.3 45 90-146 212-256 (271)
33 PRK15128 23S rRNA m(5)C1962 me 78.3 5.3 0.00011 35.3 5.6 51 93-148 4-55 (396)
34 PRK01550 truB tRNA pseudouridi 77.1 6.1 0.00013 33.8 5.5 48 91-148 240-287 (304)
35 PRK02755 truB tRNA pseudouridi 75.0 7.7 0.00017 33.1 5.5 46 91-148 234-279 (295)
36 cd02573 PseudoU_synth_EcTruB P 66.6 15 0.00032 31.1 5.4 45 91-147 232-276 (277)
37 PRK04099 truB tRNA pseudouridi 64.6 14 0.0003 31.2 4.8 45 91-148 214-258 (273)
38 PRK01851 truB tRNA pseudouridi 61.9 21 0.00046 30.5 5.5 46 91-148 245-290 (303)
39 PRK03287 truB tRNA pseudouridi 61.7 19 0.00041 30.8 5.1 44 91-148 239-282 (298)
40 PRK04642 truB tRNA pseudouridi 55.8 30 0.00065 29.6 5.4 45 91-148 242-286 (300)
41 PRK05389 truB tRNA pseudouridi 53.6 41 0.00089 28.8 5.9 48 91-148 244-291 (305)
42 PF01191 RNA_pol_Rpb5_C: RNA p 46.4 25 0.00055 23.7 2.8 29 88-136 31-59 (74)
43 PRK09570 rpoH DNA-directed RNA 45.3 22 0.00048 24.4 2.4 29 89-137 35-63 (79)
44 PF01878 EVE: EVE domain; Int 43.0 43 0.00094 24.7 4.0 25 125-149 39-65 (143)
45 COG1374 NIP7 Protein involved 43.0 32 0.00069 27.1 3.3 71 77-156 87-158 (176)
46 COG2012 RPB5 DNA-directed RNA 42.2 21 0.00046 24.4 1.9 30 88-137 37-66 (80)
47 PRK14122 tRNA pseudouridine sy 42.1 54 0.0012 28.2 4.9 43 91-148 257-299 (312)
48 PRK04980 hypothetical protein; 36.6 80 0.0017 22.6 4.3 25 124-148 30-54 (102)
49 COG4103 Uncharacterized protei 35.6 29 0.00063 26.5 2.0 30 14-43 43-72 (148)
50 PRK14123 tRNA pseudouridine sy 34.2 1.1E+02 0.0024 26.2 5.6 49 91-148 241-290 (305)
51 smart00841 Elong-fact-P_C Elon 31.3 57 0.0012 20.8 2.6 25 104-138 26-50 (56)
52 PF09285 Elong-fact-P_C: Elong 31.1 50 0.0011 21.0 2.3 29 104-143 26-54 (56)
53 PF15477 SMAP: Small acidic pr 30.4 76 0.0016 20.8 3.2 23 11-33 33-55 (69)
54 PF10262 Rdx: Rdx family; Int 28.5 1.8E+02 0.0038 19.1 5.0 53 21-84 17-69 (76)
55 TIGR03170 flgA_cterm flagella 27.4 1.7E+02 0.0038 20.7 5.0 56 101-167 46-102 (122)
56 PRK12618 flgA flagellar basal 26.4 1.9E+02 0.0041 21.7 5.1 55 102-167 63-118 (141)
57 PRK06005 flgA flagellar basal 26.2 1.5E+02 0.0034 22.7 4.7 58 100-168 80-138 (160)
58 cd04710 BAH_fungalPHD BAH, or 24.3 74 0.0016 23.8 2.5 25 125-149 11-35 (135)
59 cd05794 S1_EF-P_repeat_2 S1_EF 24.2 92 0.002 19.8 2.6 28 104-142 26-53 (56)
60 PRK02484 truB tRNA pseudouridi 23.8 2.1E+02 0.0045 24.4 5.4 43 91-148 240-282 (294)
61 PF13636 Nol1_Nop2_Fmu_2: pre- 22.9 2.3E+02 0.0049 19.8 4.8 69 65-148 19-89 (102)
62 PRK12617 flgA flagellar basal 22.9 1.8E+02 0.0039 23.6 4.7 57 101-168 136-193 (214)
63 cd00949 FBP_aldolase_I_bact Fr 22.8 67 0.0015 27.3 2.2 37 78-115 83-121 (292)
64 PRK08515 flgA flagellar basal 22.8 1.5E+02 0.0033 23.9 4.3 56 102-168 147-203 (222)
65 PF04014 Antitoxin-MazE: Antid 22.0 1.2E+02 0.0026 17.9 2.8 17 125-141 20-36 (47)
66 CHL00141 rpl24 ribosomal prote 22.0 1.5E+02 0.0033 20.2 3.6 13 125-138 8-20 (83)
67 COG3526 Uncharacterized protei 20.6 3.1E+02 0.0067 19.1 5.2 50 24-84 25-74 (99)
68 PF13144 SAF_2: SAF-like 20.3 2.7E+02 0.0058 21.5 5.2 40 123-168 137-177 (196)
69 PLN03111 DNA-directed RNA poly 20.2 85 0.0018 25.4 2.2 28 89-136 164-191 (206)
No 1
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-47 Score=291.52 Aligned_cols=180 Identities=66% Similarity=1.096 Sum_probs=173.8
Q ss_pred CCCCCCC-CCcccccccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcch
Q 030201 1 MFKKFSA-EEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMP 79 (181)
Q Consensus 1 MFkK~~~-~~~k~~~~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~P 79 (181)
||||+.+ ..+++++++|+|-+|-+|+.+.++||.++..+++++|+|+++.+.||.+|..+|.++|+++||+.++|.|+|
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 8999876 678999999999999999999999998877889999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCC
Q 030201 80 TLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAIN 159 (181)
Q Consensus 80 Tl~~l~~~p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~ 159 (181)
|+++|++||..+|.+.||.+|++|+++|||+|+||++++++.+++++++|+.|+|.++++..++|||.+.||++||.+..
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 cceEEEEEEEEcccccCCCcC
Q 030201 160 KGIGVDNMHYLNDGLWKMERL 180 (181)
Q Consensus 160 kG~av~~~h~~~D~Lw~~~~~ 180 (181)
||.++++.|++||.||.+..+
T Consensus 161 KGiGIE~~H~l~DgLw~~~~~ 181 (181)
T KOG2523|consen 161 KGIGIENYHYLNDGLWKMKQL 181 (181)
T ss_pred cCCceEEEEecCCchhheecC
Confidence 999999999999999998653
No 2
>PRK14560 putative RNA-binding protein; Provisional
Probab=100.00 E-value=1.6e-42 Score=268.91 Aligned_cols=158 Identities=27% Similarity=0.497 Sum_probs=143.6
Q ss_pred CcccccccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcchhhhhhhcCC
Q 030201 9 EVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYP 88 (181)
Q Consensus 9 ~~k~~~~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~p 88 (181)
++++.++||+||+|+||+++.+|||...+. ++.....++.++.++|++||.|+||+. ++.++||+|++|++|
T Consensus 2 ~~~~~~~l~~s~~k~L~~~l~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~p~~f~~-d~~~~Ptl~~~~~~~ 73 (160)
T PRK14560 2 EVKSRHHLSKKEVKEIKEELKEKFGVDIDG-------KDAVEEVETDKKEEIYLVDGEPLFFKV-DDELFPTLRGALKLK 73 (160)
T ss_pred ccccccccCHHHHHHHHHHHHHHcCCCccc-------cccEEEEEcCCcEEEEEECCEEEEEEe-CCcccccHHHHHhCC
Confidence 478999999999999999999999854211 334556677889999999999999988 678999999999999
Q ss_pred CCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 89 ~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
..+|+|+||++|+++|++|||||+|||++ .+++|++||+|+|++++++.++|||++.+|+++|....+|+||+++|
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 67799999999999977689999999999999999899999999999
Q ss_pred EEcccccCCC
Q 030201 169 YLNDGLWKME 178 (181)
Q Consensus 169 ~~~D~Lw~~~ 178 (181)
++||+||++.
T Consensus 150 ~~~D~lw~~~ 159 (160)
T PRK14560 150 HVGDEIWEFE 159 (160)
T ss_pred EcCchhhccc
Confidence 9999999975
No 3
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-42 Score=263.13 Aligned_cols=159 Identities=35% Similarity=0.598 Sum_probs=147.9
Q ss_pred CcccccccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcchhhhhhhcCC
Q 030201 9 EVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYP 88 (181)
Q Consensus 9 ~~k~~~~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~p 88 (181)
++++++.|++.|.|+|.+.+...|+ +.+|.+.++++.++.++..+|++||.|++|+.++ .+||||++|++++
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 4678889999999999999987776 3578888899999999999999999999999864 7999999999998
Q ss_pred CCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 89 ~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
.-.+.|+||.||++||+||||+|+|||++ ++++|++||.|.|..++++.|+|||+|+||+.||....||+||+++|
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 030201 169 YLNDGLWKMER 179 (181)
Q Consensus 169 ~~~D~Lw~~~~ 179 (181)
++||.||++..
T Consensus 150 hvGD~lw~~~~ 160 (161)
T COG2016 150 HVGDKLWEASV 160 (161)
T ss_pred ccChHHHhhhc
Confidence 99999999754
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=1.3e-40 Score=255.74 Aligned_cols=149 Identities=30% Similarity=0.543 Sum_probs=137.9
Q ss_pred cccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcchhhhhhhcCCCCccE
Q 030201 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKK 93 (181)
Q Consensus 14 ~~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~p~~lp~ 93 (181)
++++++|+|+|++.+.++||. +|++..++..++ ++.++|++||.|+||+. ++.++||++++|++|..+|+
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 579999999999999999982 468888888885 44689999999999988 57899999999999999999
Q ss_pred EEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEEccc
Q 030201 94 LQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDG 173 (181)
Q Consensus 94 v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~~~D~ 173 (181)
|+||++|+++|++|||||+|||++ ++++|++||+|+|++++++.++|||++.+|+++|....+|+||+++|++||+
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 6789999999999997779999999999999999989999999999999999
Q ss_pred ccC
Q 030201 174 LWK 176 (181)
Q Consensus 174 Lw~ 176 (181)
||+
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=8.8e-37 Score=262.40 Aligned_cols=173 Identities=29% Similarity=0.440 Sum_probs=149.9
Q ss_pred CCCCCCCCCcccccccCHHHHHHHHHHHHhHCCCC-cchhcccCCCCCcEEEEEeeCceEE-EEECCEEEEEEec-CCCc
Q 030201 1 MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGL-EPVLDDLLPKKSPLIVAKCQNHLNL-VLVNNVPLFFNIR-DGPY 77 (181)
Q Consensus 1 MFkK~~~~~~k~~~~l~~sd~kkLr~~~~~~f~~~-~~~~~~llp~~~~v~~~k~~~~~~~-y~~dg~pl~f~~~-~~~~ 77 (181)
||||. +++|++++||||||||||++. .++.+ ++..+.+.|.+.++.++|+.+...+ |..+|.||+|+.+ +|.+
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--FHVKSNTNLKNSDRKKLRQRT--FQPQLGNEEYSFRTPTKKQTNLNKFKSVGTVYYDEGGTPILFEEKHNGQL 76 (560)
T ss_pred CCCcc--cchhcccccccchHHHHHHhh--cccccCchhhhhcCCceeEEEeeeeeeeeEEEEecCCceEEEEEcCCCcc
Confidence 99998 999999999999999999943 23322 2678888999999999999877655 4567899999986 4579
Q ss_pred chhhhhhhcCCCCccEEEECcchhh-hhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHh
Q 030201 78 MPTLRLLHQYPNIMKKLQVDRGAIK-FVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIK 156 (181)
Q Consensus 78 ~PTl~~l~~~p~~lp~v~v~~~a~~-~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~ 156 (181)
|||||+||.+|.++|.+.+|.-+++ ++.+||+||.-|...+ .+|.++.|++++|...++..|+|||++.||++||.
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 5667877777776664 45789999999999999999999999999999997
Q ss_pred c-CCcceEEEEEEEEcccccCCCcC
Q 030201 157 A-INKGIGVDNMHYLNDGLWKMERL 180 (181)
Q Consensus 157 ~-~~kG~av~~~h~~~D~Lw~~~~~ 180 (181)
. +.+|+|++++|+|.|.||+.++.
T Consensus 154 v~GlkGkav~ilH~frD~Lw~sgp~ 178 (560)
T KOG2522|consen 154 VIGLKGKAVKILHHFRDGLWKSGPM 178 (560)
T ss_pred HhccccceEEEEeehhhhhhhcCCC
Confidence 7 89999999999999999998863
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=2.2e-29 Score=183.14 Aligned_cols=107 Identities=34% Similarity=0.611 Sum_probs=99.6
Q ss_pred EEECCEEEEEEecCCCcchhhhhhhcCCCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCC
Q 030201 61 VLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ 140 (181)
Q Consensus 61 y~~dg~pl~f~~~~~~~~PTl~~l~~~p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~ 140 (181)
|++||.|++|... +.++||++++|++|..+|+|+||++|+++|++||+||+|||++ .+++|++||+|+|++.+++
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 4789999999999999999999999999999999999999998 6678999999999986668
Q ss_pred eEEEEEEEecCHHHHhcCCcceEEEEEEEEcc
Q 030201 141 HALAIGFTKMSAKDIKAINKGIGVDNMHYLND 172 (181)
Q Consensus 141 ~~vaVG~~~~~~~~i~~~~kG~av~~~h~~~D 172 (181)
.++|+|++.+|++||....+|+|++++|++||
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=99.90 E-value=2.9e-23 Score=190.12 Aligned_cols=150 Identities=17% Similarity=0.158 Sum_probs=128.8
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEE-EEecCCCcchhhhhhhcC----CC
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRLLHQY----PN 89 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~l~~~----p~ 89 (181)
..++.|.+.|++.+.+|||.. ..+.++|++..+..+|-+++.+.+++||.+++ ++..++.++||++++.+. |.
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 568999999999999999842 33557888876666665677888899999997 776778899999765443 33
Q ss_pred CccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEE
Q 030201 90 IMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHY 169 (181)
Q Consensus 90 ~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~ 169 (181)
..++|+||++|++++.+|||||+|||++ ++++|++||+|.|+. +++.++|||+|+||++||....+|+||+++|.
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 030201 170 LN 171 (181)
Q Consensus 170 ~~ 171 (181)
..
T Consensus 637 ~~ 638 (639)
T PRK13534 637 VK 638 (639)
T ss_pred CC
Confidence 64
No 8
>PRK13795 hypothetical protein; Provisional
Probab=99.87 E-value=2.5e-21 Score=178.08 Aligned_cols=146 Identities=20% Similarity=0.332 Sum_probs=124.3
Q ss_pred cccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEe--eCceEEEEECCEE---EEEEecCCC--cchhhhh---
Q 030201 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKC--QNHLNLVLVNNVP---LFFNIRDGP--YMPTLRL--- 83 (181)
Q Consensus 14 ~~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~--~~~~~~y~~dg~p---l~f~~~~~~--~~PTl~~--- 83 (181)
-+-..+|++.|++.+.+|||.. ++|++..+.++|+ ++++++|++||.+ ++|+..++. +.||+++
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 3467899999999999999842 1667777888987 5788999999998 456655444 5688864
Q ss_pred hhcCCCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceE
Q 030201 84 LHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIG 163 (181)
Q Consensus 84 l~~~p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~a 163 (181)
|++ +...++|+||++|+++|++||+||+|||++ ++++|++||.|+|++ +++.++|||++.+|+++|....+|++
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 030201 164 VDNMHYLN 171 (181)
Q Consensus 164 v~~~h~~~ 171 (181)
|+++|...
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=2.8e-20 Score=166.19 Aligned_cols=145 Identities=17% Similarity=0.278 Sum_probs=120.6
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEee--CceEEEEECCEEE---EEEecCCC--cchhhhhhhcC
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQ--NHLNLVLVNNVPL---FFNIRDGP--YMPTLRLLHQY 87 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~--~~~~~y~~dg~pl---~f~~~~~~--~~PTl~~l~~~ 87 (181)
+-...|.+.|+..+.+|||. +++|++..+.++|+. +++..+++||.++ +|+..++. +.||+..+..+
T Consensus 45 ~a~~~d~~~i~~i~~~qFG~------~l~p~~~~vllnK~~~~~~~~eVi~dg~~l~~l~~~~~~~~w~~~l~~~ga~~l 118 (479)
T PRK13794 45 PAFKYDIDLINKILEEQFGI------ENIPEGKIVLLNKVPGIERMEEIIVDGAVVGIIRYNEKKHRWKIIPRPEGARRL 118 (479)
T ss_pred cCChHHHHHHHHHHHHHcCC------cccCCCcEEEEecCCCCCcceEEEECCEEEEEEEeccccceeEEecCHHHHHHh
Confidence 45689999999999999994 478988888888984 5667778999986 56666665 46776554333
Q ss_pred CCC--ccEEEECcchhhhhh-cCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEE
Q 030201 88 PNI--MKKLQVDRGAIKFVL-SGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGV 164 (181)
Q Consensus 88 p~~--lp~v~v~~~a~~~i~-~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av 164 (181)
... .++|+||++|+++|+ +||+||+|||++ ++++|++||.|+|++ .++.++|||++.+|+++|....+|+||
T Consensus 119 ~~~~~~~~V~Vd~ga~~~v~~~G~~v~~~GV~~----~~~~i~~gd~V~Iv~-~~g~~iavG~a~~s~~ei~~~~~G~~V 193 (479)
T PRK13794 119 IPTAKKKFIVVKDDVPKFIRNKGASVLRPGVAE----ASEDIEEGDDVIILD-ENGDVVGVGRARMSYEEIVNMEKGMVV 193 (479)
T ss_pred hhccCCcEEEECccHHHHHHhCCCeecCCceEE----ecCCcCCCCEEEEEc-CCCcEEEEEEeecCHHHHHhccCceEE
Confidence 111 357999999999999 999999999999 778999999999998 457899999999999999999999999
Q ss_pred EEEEEE
Q 030201 165 DNMHYL 170 (181)
Q Consensus 165 ~~~h~~ 170 (181)
+++|.-
T Consensus 194 kvr~~~ 199 (479)
T PRK13794 194 KVRKSE 199 (479)
T ss_pred EEEecc
Confidence 999943
No 10
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.83 E-value=9.6e-20 Score=137.20 Aligned_cols=146 Identities=19% Similarity=0.333 Sum_probs=124.2
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEE-EEecCCCcchhhhh---hhcC-CC
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRL---LHQY-PN 89 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~---l~~~-p~ 89 (181)
+..+.+.+++|..+.+|||. +..+.++|++..+.+. -+++.+.++.+|++++ .+.+||.+.||++. ||+. |.
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 35678999999999999995 4677899999766533 3788888889999885 56678888899965 4542 22
Q ss_pred CccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 90 IMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 90 ~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
.--+|+|.+.+.+|+.+|.++|+.-|+. .++++++||+|+|+. .+++++|+|++++|..||...+.|.||++..
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 2338999999999999999999999999 899999999999998 6689999999999999999999999999864
No 11
>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=99.78 E-value=3.1e-19 Score=121.64 Aligned_cols=74 Identities=32% Similarity=0.573 Sum_probs=67.2
Q ss_pred cEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030201 92 KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (181)
Q Consensus 92 p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~~ 170 (181)
|+|+||++|+++|++||+||+|||++ ++++|++||+|.|.+ .++.++|+|++.+|+++|....+|+++++.|++
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 778899999999999 558999999999999999999999999999974
No 12
>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=99.78 E-value=2.3e-18 Score=155.08 Aligned_cols=145 Identities=12% Similarity=0.139 Sum_probs=122.6
Q ss_pred cCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEE-EEecCCCcchhhhhhhcC----CCC
Q 030201 16 VKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRLLHQY----PNI 90 (181)
Q Consensus 16 l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~l~~~----p~~ 90 (181)
.++.+..++|..+.+|||. ...+++||++..+..+|.+++...++.+|..++ ++.+||.+.||++...+. +..
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 3667888999999999995 346789999876766666788877777887664 566788899999664332 333
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNM 167 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~ 167 (181)
-.+|+|++.+++++..|.++++|||++ ++++|++||+|+|+. ++++.+|||+|.||+.||....+|.||+++
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 459999999999999999999999999 899999999999997 557999999999999999999999999987
No 13
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=99.60 E-value=9.7e-15 Score=113.73 Aligned_cols=141 Identities=20% Similarity=0.354 Sum_probs=116.8
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEee--CceEEEEECCEE---EEEEecCCCcc--hhh---hhh
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQ--NHLNLVLVNNVP---LFFNIRDGPYM--PTL---RLL 84 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~--~~~~~y~~dg~p---l~f~~~~~~~~--PTl---~~l 84 (181)
+-..+|+.-+|+.+.+.||. ..+++++..+.++|+. +...++++||.. ++|+.+...|- |.+ ..|
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 35678999999999999984 2457777889999995 567888899964 57888766664 444 334
Q ss_pred hcCCCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEE
Q 030201 85 HQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGV 164 (181)
Q Consensus 85 ~~~p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av 164 (181)
|.. ....+.++.++.+++.||+|+.+|||++ +..++++||.|+|.+ .++.++|||++.+|++++....+|++|
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 LEK--GKKGRKIDRGAVEPVKNGKNVLPPGVIE----AEDSIERGDEVIVVS-ENGRVVGVGIAKKSYEELINPERGTGV 196 (202)
T ss_pred HHh--cCccEEEEcccchhhhccCcccCCceee----ccCCcccCCeEEEEe-cCCEEEEEEEEecCHHHhcCcccCccc
Confidence 432 1567899999999999999999999999 778999999999988 789999999999999999998899999
Q ss_pred EEE
Q 030201 165 DNM 167 (181)
Q Consensus 165 ~~~ 167 (181)
++.
T Consensus 197 ~~~ 199 (202)
T COG5270 197 KPR 199 (202)
T ss_pred CCC
Confidence 865
No 14
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=99.26 E-value=2.8e-11 Score=81.97 Aligned_cols=74 Identities=32% Similarity=0.572 Sum_probs=66.9
Q ss_pred EEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcC--CcceEEEEEEEE
Q 030201 93 KLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAI--NKGIGVDNMHYL 170 (181)
Q Consensus 93 ~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~--~kG~av~~~h~~ 170 (181)
++++++.+.+++++|++||.+||.. .++++++||+|.|++ .++.++|+|.+..++.++... .+|.++++.|++
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 030201 171 N 171 (181)
Q Consensus 171 ~ 171 (181)
.
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=99.20 E-value=7.6e-11 Score=100.77 Aligned_cols=78 Identities=28% Similarity=0.479 Sum_probs=70.9
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~~ 170 (181)
+|.+.+++.+++++.+|++++.||+.. .+..+..|+.|.|+. .++.++|||++.+|+++|....+|++|++.|.+
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 555578899998887 457999999999999999998999999999999
Q ss_pred ccc
Q 030201 171 NDG 173 (181)
Q Consensus 171 ~D~ 173 (181)
+|.
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=99.11 E-value=3e-10 Score=96.33 Aligned_cols=76 Identities=25% Similarity=0.398 Sum_probs=69.3
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~~ 170 (181)
+|.+.+++++++++.+|++++.||+.. .+.++.+||.|.|+. .++.++|+|++.++++++....+|++|++.|++
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 455678899999987 467999999999999999999999999999998
Q ss_pred c
Q 030201 171 N 171 (181)
Q Consensus 171 ~ 171 (181)
+
T Consensus 300 ~ 300 (300)
T PRK04270 300 M 300 (300)
T ss_pred C
Confidence 5
No 17
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=98.97 E-value=2.3e-09 Score=93.47 Aligned_cols=64 Identities=20% Similarity=0.385 Sum_probs=59.0
Q ss_pred CCccEEEECcchhhhh-hcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhc
Q 030201 89 NIMKKLQVDRGAIKFV-LSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (181)
Q Consensus 89 ~~lp~v~v~~~a~~~i-~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~ 157 (181)
...+.|+||++|+++| ++||+|++|||++ +..+|++||.|.|.+ .+++++|+|++.+|++|+..
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 3568999999999999 8999999999999 778999999999998 66899999999999999976
No 18
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=98.92 E-value=7.1e-09 Score=91.90 Aligned_cols=69 Identities=19% Similarity=0.325 Sum_probs=59.1
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~~ 170 (181)
..+|-||+... --++++|||++ ++++|++||+|.|+- +++..|||+|.||+.+|....||.||+++|+.
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 45677776532 35899999999 889999999997753 37999999999999999999999999999985
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=98.70 E-value=5.9e-08 Score=84.42 Aligned_cols=63 Identities=17% Similarity=0.369 Sum_probs=57.3
Q ss_pred CccEEEECcchhhhhhc-CCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhc
Q 030201 90 IMKKLQVDRGAIKFVLS-GANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (181)
Q Consensus 90 ~lp~v~v~~~a~~~i~~-GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~ 157 (181)
..+.|+||++|+++|.+ |++||.+||++ +..+|.+||.|.|++ .++.++|.|.+.+|++|+..
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 45699999999999975 99999999999 677999999999998 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=98.49 E-value=5.3e-07 Score=59.26 Aligned_cols=63 Identities=21% Similarity=0.427 Sum_probs=41.8
Q ss_pred ccccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcchhhhhhhcC
Q 030201 13 QNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQY 87 (181)
Q Consensus 13 ~~~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~ 87 (181)
.+.||..|+|.+.+.+.+-||.. ++. +.|++.+ +.+...|++||.|+||.. .++||||+|.++
T Consensus 2 RH~LSkKe~k~~~~k~~~~ygId-------i~~-~~vEI~~-~kk~~~yyi~~~p~ff~~---~lIPtL~~l~k~ 64 (65)
T PF09183_consen 2 RHFLSKKEIKEIKEKIKEKYGID-------ISG-EKVEIGK-EKKFSIYYIDGVPAFFND---KLIPTLCFLNKH 64 (65)
T ss_dssp -EE--HHHHHHHHHHHHT-TT----------TT----EEEE--SS-EEEEETTEEEEEES---SEEE-HHHHHHS
T ss_pred cccccHHHHHHHHHHHHHHhCcC-------CCc-cceeeee-ccceEEEEECCchhhhcC---CcchhhhhHhhc
Confidence 45699999999999999889832 223 3477776 444568999999999863 699999999865
No 21
>PRK08557 hypothetical protein; Provisional
Probab=98.33 E-value=2.3e-06 Score=75.72 Aligned_cols=127 Identities=16% Similarity=0.178 Sum_probs=92.2
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEee--CceEEEEECCEE---EEEEecCCCc--chhhhhhhcC
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQ--NHLNLVLVNNVP---LFFNIRDGPY--MPTLRLLHQY 87 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~--~~~~~y~~dg~p---l~f~~~~~~~--~PTl~~l~~~ 87 (181)
+-...|++.|++.+.++|+.. . .+.++|+. +++..+++||.. +.|+..+..+ .|+...+. .
T Consensus 8 ~a~~~d~~~~~~~~~~~f~~~-----~------~vllnk~p~~d~~~ev~~~g~~~g~~~~~~~~~~w~~~p~~~~~~-~ 75 (417)
T PRK08557 8 FASPYEIKILNKLTNKNFQYD-----D------AIILEKLSGLDYRKRVYISEDQIGILEFDLLDLDWKFHPSPSYYL-I 75 (417)
T ss_pred cCCHHHHHHHHHHHHHHcCCC-----e------EEEEeCCCCccchhheeECCeEEEEEEEccccceeEEccchhhhh-c
Confidence 356899999999999999831 1 37888984 678889999975 4566644443 56654321 1
Q ss_pred CCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcce
Q 030201 88 PNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGI 162 (181)
Q Consensus 88 p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~ 162 (181)
. -+.|.++. +.++| +|+++..++|.+... + +++++||.|+|.. +..+|||++.++...+....+|.
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 46788886 66777 999999999987332 2 3799999888866 67999999999776665555544
No 22
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=97.99 E-value=2e-05 Score=68.74 Aligned_cols=63 Identities=10% Similarity=0.118 Sum_probs=56.8
Q ss_pred CccEEEECcchhhhhh-cCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhc
Q 030201 90 IMKKLQVDRGAIKFVL-SGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (181)
Q Consensus 90 ~lp~v~v~~~a~~~i~-~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~ 157 (181)
....++||++|.++|. +|++|+..||+. +...|.+||.|.|+. .++..+|.|.+..||+|+..
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 3469999999999996 689999999999 667899999999998 66899999999999999865
No 23
>PF14810 TGT_C2: Patch-forming domain C2 of tRNA-guanine transglycosylase; PDB: 1J2B_A 1IT8_A 1IT7_B 1IQ8_A.
Probab=97.86 E-value=2.2e-05 Score=53.35 Aligned_cols=61 Identities=21% Similarity=0.249 Sum_probs=40.1
Q ss_pred HHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEE-EEecCCCcchhhhhh
Q 030201 22 RKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRLL 84 (181)
Q Consensus 22 kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~l 84 (181)
+.||..+.+|||. ...++|+|++..+...+-+.+.+.++.||+.++ ++.+||.+.||++..
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 357789999976766666788888888998653 445788899999664
No 24
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=97.39 E-value=0.00036 Score=60.25 Aligned_cols=61 Identities=23% Similarity=0.426 Sum_probs=54.6
Q ss_pred ccEEEECcchhhhhh-cCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhc
Q 030201 91 MKKLQVDRGAIKFVL-SGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (181)
Q Consensus 91 lp~v~v~~~a~~~i~-~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~ 157 (181)
-..|++|.+|.++|. +|.+|..-||+. +..+|..||.|.|+ .++..+|=|.+..|++|+..
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 469999999999998 899999999999 66789999999999 33559999999999999865
No 25
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.18 E-value=0.018 Score=49.20 Aligned_cols=74 Identities=11% Similarity=0.159 Sum_probs=59.0
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhc----CCcceEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA----INKGIGVDN 166 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~----~~kG~av~~ 166 (181)
+|.+.+++...+.+.+|+.+-.+++.. . .++..++.+.+.. .++.++|+|.+..++..+.. ..+|.+++.
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 789999999999999999997776644 2 2456688888877 46889999999888876554 345999998
Q ss_pred EEEE
Q 030201 167 MHYL 170 (181)
Q Consensus 167 ~h~~ 170 (181)
.+.+
T Consensus 302 ~~v~ 305 (308)
T PRK14124 302 KKVF 305 (308)
T ss_pred eeee
Confidence 8876
No 26
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.81 E-value=0.005 Score=53.93 Aligned_cols=77 Identities=19% Similarity=0.358 Sum_probs=68.5
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i~~~~kG~av~~~h~~ 170 (181)
..++++.+++++.+|.||.+|.||+.. .++++.-+..+++.+ .+++.++.+.+.++..++....+|...++..++
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 667888889999988 678999999999999999999999888888775
Q ss_pred cc
Q 030201 171 ND 172 (181)
Q Consensus 171 ~D 172 (181)
+.
T Consensus 350 me 351 (395)
T KOG2529|consen 350 ME 351 (395)
T ss_pred cc
Confidence 43
No 27
>KOG3492 consensus Ribosome biogenesis protein NIP7 [Translation, ribosomal structure and biogenesis]
Probab=92.33 E-value=1.6 Score=33.71 Aligned_cols=143 Identities=15% Similarity=0.265 Sum_probs=93.5
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEEC-----------CEEE------E--EEecCC
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVN-----------NVPL------F--FNIRDG 75 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~d-----------g~pl------~--f~~~~~ 75 (181)
+|+..|.|-+-+.+..-.|. .+..|+...+.--..+.... ++|++. +.++ | |. ..+
T Consensus 3 ~Lt~Eetk~vfekla~yIG~---Nv~~lidr~D~~~cfrlhkd-RVyyvsEr~~k~a~~isr~~L~s~Gtc~GKFT-Kt~ 77 (180)
T KOG3492|consen 3 PLTEEETKVVFEKLAKYIGD---NVSHLIDRPDGTYCFRLHKD-RVYYVSERIMKLAACISRKNLVSLGTCFGKFT-KTG 77 (180)
T ss_pred CCcHHHHHHHHHHHHHHHhh---hhheeecCCCCceeeEeeCc-eEEeehHHHHHHHhhhcccceeEEeEEEeeee-ccc
Confidence 57778888888888766663 34455655554344444322 222221 1111 1 11 123
Q ss_pred Cc---chhhhhhhcCCCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCH
Q 030201 76 PY---MPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSA 152 (181)
Q Consensus 76 ~~---~PTl~~l~~~p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~ 152 (181)
.+ +-+|..|-++ ..-.|-+++++-.....|.++...||-. +.+++..++-|.|++ -++.|++.|.+..|.
T Consensus 78 kfrlhitaL~~La~~--Ak~KvWiKp~~Em~flYGNhvlKs~vgR----itd~~p~~~GVvVys-m~DvPLGFGv~Akst 150 (180)
T KOG3492|consen 78 KFRLHITALDYLAPY--AKYKVWIKPNAEMQFLYGNHVLKSGVGR----ITDGIPQHQGVVVYS-MNDVPLGFGVTAKST 150 (180)
T ss_pred eEEEeeeehhhhhhh--hheeEEeccCcccceeecccchhcccce----ecCCCCCcceEEEEe-ccCCccccceeecCc
Confidence 33 3444445433 3456778888877667999999999866 778889999999998 678999999999999
Q ss_pred HHHhcCCcceEEEEEEEE
Q 030201 153 KDIKAINKGIGVDNMHYL 170 (181)
Q Consensus 153 ~~i~~~~kG~av~~~h~~ 170 (181)
.+.. ...+.|+.++|.-
T Consensus 151 ~d~r-~~dp~aiv~~hQa 167 (180)
T KOG3492|consen 151 QDCR-KADPTAIVVLHQA 167 (180)
T ss_pred cccc-ccCCcEEEEEEec
Confidence 8865 4567788888863
No 28
>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=90.22 E-value=0.56 Score=36.49 Aligned_cols=119 Identities=16% Similarity=0.235 Sum_probs=65.7
Q ss_pred ccCHHHHHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEEC----------------CEEE-EEEecCCCc
Q 030201 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVN----------------NVPL-FFNIRDGPY 77 (181)
Q Consensus 15 ~l~~sd~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~d----------------g~pl-~f~~~~~~~ 77 (181)
+|+..|.+.+.+.+. .|+... ++... .....+.. +.++|++. |..+ -|.-....+
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-----LLDHF-DFYVFRLH-KDRVYYVSEELMKLASNRPNLYSLGTCLGKFTKKGKKF 76 (162)
T ss_dssp E--HHHHHHHHHHHH-CCCCGH-----CCEET-EEEEEECC-TCEEEEEEHHHHCCCTTCHHHHCCSEEEEEE-TTTSEE
T ss_pred CCCHHHHHHHHHHHH-Hhcchh-----hcccc-cceeeeee-cceEEEECHHHHHHHhCCCccceeceEEEEEecCCccc
Confidence 588899999998884 687421 11111 12223222 23454432 2222 122111234
Q ss_pred chhhhhhhc-CCCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 78 MPTLRLLHQ-YPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 78 ~PTl~~l~~-~p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
..++-++.- .+.....|.|.+.+....+.|.|++.-||.. +.++..+. |+|.. .++.|+|+|..
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 445544332 2444568999999988888999999999988 55555555 88887 77899999943
No 29
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=87.48 E-value=1.5 Score=37.22 Aligned_cols=50 Identities=18% Similarity=0.289 Sum_probs=38.6
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..++.+++|+.+-.+++.. .+..++.+.+.. .++.++|+|..
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 689999999999999999986655432 244567777776 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=86.14 E-value=2.7 Score=26.42 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=30.4
Q ss_pred cEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEe
Q 030201 92 KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTK 149 (181)
Q Consensus 92 p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~ 149 (181)
|.|.+++.....+++|-.+-... .....| .|.|++ .++.++|+|...
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 67899999999999999874411 123445 999996 668999999874
No 31
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=81.25 E-value=3.9 Score=35.15 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=35.3
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..+..+++|+.+..+++ ..++.|.+....++.++|+|..
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 32
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=80.70 E-value=2.7 Score=35.43 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=35.0
Q ss_pred CccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEE
Q 030201 90 IMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIG 146 (181)
Q Consensus 90 ~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG 146 (181)
.+|++.+++.++..+++|+. ||+.. +.+|+.|+|.++. +..+|+|
T Consensus 212 ~lpk~~i~~~~~~~i~~G~~---~~~~~--------~~~~~~v~v~~~~-~~~~al~ 256 (271)
T COG0130 212 DLPRLVLKDSAANAIKYGAK---PGLLD--------IELGGLVRVYTAK-GLGIALG 256 (271)
T ss_pred cCCcEecCHHHHHHHHcCCc---hhccc--------cccCCcEEEEccC-CeEEEEe
Confidence 36899999999999999999 77643 6789999999844 5333433
No 33
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=78.33 E-value=5.3 Score=35.35 Aligned_cols=51 Identities=16% Similarity=0.243 Sum_probs=39.2
Q ss_pred EEEECcchhhhhhcCCc-ccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 93 KLQVDRGAIKFVLSGAN-IMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 93 ~v~v~~~a~~~i~~GAd-Lm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+++++.++.+.+.+|.. +|..-|.. ..+++.+|++|.|.+ .++.++|.|..
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 46788888888988886 55555543 334688999999998 66899999976
No 34
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=77.13 E-value=6.1 Score=33.82 Aligned_cols=48 Identities=23% Similarity=0.277 Sum_probs=36.0
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..++.+++|+.+..++... ..++.+.+.. .++.++|+|..
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 2245566666 45789999975
No 35
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=75.02 E-value=7.7 Score=33.07 Aligned_cols=46 Identities=17% Similarity=0.236 Sum_probs=35.0
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..+..+++|+.+..+. +..++.+.+.. .++.++|+|..
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 689999999999999999984322 23356677766 45789999965
No 36
>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=66.64 E-value=15 Score=31.06 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=34.2
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGF 147 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~ 147 (181)
+|.+.+++...+.+++|+.+-.+++ ..++.+.+.. .++.++|+|.
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 37
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=64.56 E-value=14 Score=31.21 Aligned_cols=45 Identities=9% Similarity=-0.062 Sum_probs=33.6
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|++.+.+ .++.|++|+-++.+|+.. . +...+.+.. +.++||+..
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 57888888 899999999999999754 1 224566652 458888765
No 38
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=61.89 E-value=21 Score=30.53 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=34.4
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..++.+++|+.+-.. .+..++.|.+.. .++.++|||..
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=61.69 E-value=19 Score=30.81 Aligned_cols=44 Identities=9% Similarity=0.090 Sum_probs=33.2
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..++.+++|+.+-.++ .++.+.+.. .++.++|+|..
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 699999999999999999884322 124466665 45789999974
No 40
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=55.84 E-value=30 Score=29.63 Aligned_cols=45 Identities=11% Similarity=0.194 Sum_probs=33.1
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..+..+++|+.+-.+. +. .+.+.+.. .++.++|+|..
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 689999999999999999983221 11 24566665 46789999965
No 41
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=53.56 E-value=41 Score=28.85 Aligned_cols=48 Identities=15% Similarity=0.163 Sum_probs=32.6
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..++.+++|+.+-.++. ... ..+..+.+ . .++.++|+|..
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 000 11224444 3 45789999975
No 42
>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=46.43 E-value=25 Score=23.72 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=22.9
Q ss_pred CCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEe
Q 030201 88 PNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMA 136 (181)
Q Consensus 88 p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~ 136 (181)
+.-||++...|++++++ ++++||+|-|.-
T Consensus 31 ~~qLP~I~~~DPv~r~~--------------------g~k~GdVvkI~R 59 (74)
T PF01191_consen 31 PEQLPKILSSDPVARYL--------------------GAKPGDVVKIIR 59 (74)
T ss_dssp TTCSSEEETTSHHHHHT--------------------T--TTSEEEEEE
T ss_pred hhhCCcccccChhhhhc--------------------CCCCCCEEEEEe
Confidence 56689999999999887 567899998865
No 43
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=45.28 E-value=22 Score=24.36 Aligned_cols=29 Identities=10% Similarity=0.225 Sum_probs=23.6
Q ss_pred CCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeC
Q 030201 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAE 137 (181)
Q Consensus 89 ~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~ 137 (181)
.-||++..+|++++++ ++++||+|-|.-.
T Consensus 35 ~qLP~I~~~DPv~r~~--------------------g~k~GdVvkI~R~ 63 (79)
T PRK09570 35 EQLPKIKASDPVVKAI--------------------GAKPGDVIKIVRK 63 (79)
T ss_pred HHCCceeccChhhhhc--------------------CCCCCCEEEEEEC
Confidence 4589999999998886 5678999999763
No 44
>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=43.03 E-value=43 Score=24.74 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=16.6
Q ss_pred CCCCCCeEEEEeCC--CCeEEEEEEEe
Q 030201 125 EVGAETPVAIMAEG--KQHALAIGFTK 149 (181)
Q Consensus 125 ~i~~Gd~V~V~~~~--~~~~vaVG~~~ 149 (181)
.+++||.|.++..+ ...++|+|+..
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 34677777774
No 45
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=42.98 E-value=32 Score=27.14 Aligned_cols=71 Identities=17% Similarity=0.230 Sum_probs=44.6
Q ss_pred cchhhhhhhcCCCCccEEEECcch-hhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEEecCHHHH
Q 030201 77 YMPTLRLLHQYPNIMKKLQVDRGA-IKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDI 155 (181)
Q Consensus 77 ~~PTl~~l~~~p~~lp~v~v~~~a-~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~~~~~~~i 155 (181)
.++.+..|.++- .-.+.+...+ +.|+ -|-| ..-++.+ +..++.....|.|+. .|+.|.++|....|+.+.
T Consensus 87 ~~~~l~~la~~~--~~k~~v~~~~e~~FL-Yg~~-lkd~~~e----~~~~~~~~~~v~V~~-~nd~~lgiGvg~~s~~ed 157 (176)
T COG1374 87 HVESLEELARIA--IIKNYVKERGEMLFL-YGND-LKDHVKE----IIDEIPENGGVFVFN-MNDVPLGIGVGALSPSED 157 (176)
T ss_pred ehhhhHHHHHHh--heeeeeccCceeEEE-eccc-cchhhhh----hccccCCcceEEEEE-cCCCceEEEecccCchhh
Confidence 356665554432 3344444443 3444 5665 3344444 445677778888887 789999999999987764
Q ss_pred h
Q 030201 156 K 156 (181)
Q Consensus 156 ~ 156 (181)
.
T Consensus 158 ~ 158 (176)
T COG1374 158 G 158 (176)
T ss_pred c
Confidence 3
No 46
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=42.17 E-value=21 Score=24.40 Aligned_cols=30 Identities=17% Similarity=0.247 Sum_probs=23.9
Q ss_pred CCCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeC
Q 030201 88 PNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAE 137 (181)
Q Consensus 88 p~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~ 137 (181)
|.-||+|..+|++++++ +.+.||+|-|...
T Consensus 37 ~~qLPkI~~~DPva~~l--------------------gak~GdvVkIvRk 66 (80)
T COG2012 37 PEQLPKIKASDPVAKAL--------------------GAKPGDVVKIVRK 66 (80)
T ss_pred HHHCCcccccChhHHHc--------------------cCCCCcEEEEEec
Confidence 56789999999999876 3466898888763
No 47
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=42.10 E-value=54 Score=28.21 Aligned_cols=43 Identities=19% Similarity=0.270 Sum_probs=32.4
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++...+.+.+|..+-.+ ..+.+.+.. .++.++|+|..
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 56789999864
No 48
>PRK04980 hypothetical protein; Provisional
Probab=36.62 E-value=80 Score=22.65 Aligned_cols=25 Identities=0% Similarity=-0.166 Sum_probs=20.1
Q ss_pred cCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 124 EEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 124 ~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
..+++||.+.|.+.+.+.++++-+.
T Consensus 30 ~~~~~G~~~~V~~~e~g~~~c~ieI 54 (102)
T PRK04980 30 SHFKPGDVLRVGTFEDDRYFCTIEV 54 (102)
T ss_pred cCCCCCCEEEEEECCCCcEEEEEEE
Confidence 4689999999987778888876554
No 49
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.57 E-value=29 Score=26.52 Aligned_cols=30 Identities=20% Similarity=0.251 Sum_probs=24.3
Q ss_pred cccCHHHHHHHHHHHHhHCCCCcchhcccC
Q 030201 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLL 43 (181)
Q Consensus 14 ~~l~~sd~kkLr~~~~~~f~~~~~~~~~ll 43 (181)
-+++.+|+.++|+.+.+.|+...+.+++|+
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 468999999999999999997655565553
No 50
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=34.19 E-value=1.1e+02 Score=26.17 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=32.0
Q ss_pred ccEEEECcch-hhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGA-IKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a-~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++.. .+.+.+|+.+-.... ++. ..+..+.+.. .++.++|+|..
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 1233444443 45789999964
No 51
>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=31.33 E-value=57 Score=20.77 Aligned_cols=25 Identities=12% Similarity=0.260 Sum_probs=18.1
Q ss_pred hhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCC
Q 030201 104 VLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEG 138 (181)
Q Consensus 104 i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~ 138 (181)
|.+|+.+|.|-- |+.||.+.|.+..
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 456888888774 4568999888743
No 52
>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=31.09 E-value=50 Score=21.05 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=17.1
Q ss_pred hhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEE
Q 030201 104 VLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHAL 143 (181)
Q Consensus 104 i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~v 143 (181)
|.+|+-++.|-- ++.||.|.|.+ ..+..+
T Consensus 26 letG~~i~VP~F----------I~~Gd~I~VdT-~~g~Yv 54 (56)
T PF09285_consen 26 LETGAEIQVPLF----------IEEGDKIKVDT-RDGSYV 54 (56)
T ss_dssp ETTS-EEEEETT------------TT-EEEEET-TTTEEE
T ss_pred EcCCCEEEccce----------ecCCCEEEEEC-CCCeEe
Confidence 446787777764 55699999987 445543
No 53
>PF15477 SMAP: Small acidic protein family
Probab=30.35 E-value=76 Score=20.83 Aligned_cols=23 Identities=22% Similarity=0.397 Sum_probs=20.3
Q ss_pred ccccccCHHHHHHHHHHHHhHCC
Q 030201 11 SAQNQVKASVQRKIRQSIADEYP 33 (181)
Q Consensus 11 k~~~~l~~sd~kkLr~~~~~~f~ 33 (181)
.++..+..++.++|.+.|..||-
T Consensus 33 ~~~~~~~~~~~~~l~~~Le~Qy~ 55 (69)
T PF15477_consen 33 SPNMALSKEKQEKLQQDLEQQYE 55 (69)
T ss_pred CccccccHHHHHHHHHHHHHHHH
Confidence 46677999999999999999994
No 54
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=28.52 E-value=1.8e+02 Score=19.11 Aligned_cols=53 Identities=15% Similarity=0.255 Sum_probs=32.3
Q ss_pred HHHHHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcchhhhhh
Q 030201 21 QRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLL 84 (181)
Q Consensus 21 ~kkLr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l 84 (181)
...+++.|..+||.. + ..++.....+..-++.+||..+|=....+ -||+..-+
T Consensus 17 a~~l~~~l~~~fp~~---~-------~~v~~~~~~~G~FEV~v~g~lI~SK~~~g-~fP~~~~i 69 (76)
T PF10262_consen 17 ALELAQELLQTFPDR---I-------AEVELSPGSTGAFEVTVNGELIFSKLESG-RFPDPDEI 69 (76)
T ss_dssp HHHHHHHHHHHSTTT---C-------SEEEEEEESTT-EEEEETTEEEEEHHHHT-SSS-HHHH
T ss_pred HHHHHHHHHHHCCCc---c-------eEEEEEeccCCEEEEEEccEEEEEehhcC-CCCCHHHH
Confidence 457888899999841 1 12444444555666789999887555433 47877544
No 55
>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=27.44 E-value=1.7e+02 Score=20.71 Aligned_cols=56 Identities=14% Similarity=0.026 Sum_probs=34.3
Q ss_pred hhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEE
Q 030201 101 IKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNM 167 (181)
Q Consensus 101 ~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~-~~vaVG~~~~~~~~i~~~~kG~av~~~ 167 (181)
...|..|.-|..--+ . .++-+++||.|.|.....+ ..-+-|+|+-| +..|..|++.
T Consensus 46 ~r~i~~G~~i~~~~l-~----~~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~------g~~G~~I~V~ 102 (122)
T TIGR03170 46 KRPLRAGQPLTANML-R----PPWLVKRGDTVTVIARGGGLSVTTEGKALED------GAVGDQIRVR 102 (122)
T ss_pred ecccCCCCeeChHhc-C----CccEEcCCCEEEEEEecCCEEEEEEEEEccc------cCCCCEEEEE
Confidence 344445555533333 2 2346889999999886644 57778888654 4566666554
No 56
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.36 E-value=1.9e+02 Score=21.74 Aligned_cols=55 Identities=15% Similarity=0.020 Sum_probs=35.3
Q ss_pred hhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEE
Q 030201 102 KFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNM 167 (181)
Q Consensus 102 ~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~-~~vaVG~~~~~~~~i~~~~kG~av~~~ 167 (181)
+.|..|..+..--+-. +.=+++||.|.|...+.+ ..-+-|+|+-| +..|..|++.
T Consensus 63 R~l~aGq~i~~~~L~~-----p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~------G~~Gd~IrV~ 118 (141)
T PRK12618 63 VTLYAGRPIRAADLGP-----PAIVDRNQLVPLAYRLGGLEIRTEGRALSR------GGVGDEIRVM 118 (141)
T ss_pred eecCCCCeeCHHHcCC-----ccEEeCCCEEEEEEecCCEEEEEEEEEccc------CCCCCEEEEE
Confidence 3444555554444332 245788999999986654 67888988755 4666666654
No 57
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.18 E-value=1.5e+02 Score=22.70 Aligned_cols=58 Identities=21% Similarity=0.146 Sum_probs=38.8
Q ss_pred hhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 100 AIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 100 a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~-~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
+.+.|..|..+..--+-. +.-+++||.|.|...+++ ..-+-|+|+-| +..|..|++..
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 345566676665555443 346889999999986655 57778888654 56676666653
No 58
>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=24.29 E-value=74 Score=23.80 Aligned_cols=25 Identities=12% Similarity=0.072 Sum_probs=22.0
Q ss_pred CCCCCCeEEEEeCCCCeEEEEEEEe
Q 030201 125 EVGAETPVAIMAEGKQHALAIGFTK 149 (181)
Q Consensus 125 ~i~~Gd~V~V~~~~~~~~vaVG~~~ 149 (181)
.++.||-|.|..+..++|.-||+..
T Consensus 11 ~~~vgD~Vyv~~~~~~ePyyIgrI~ 35 (135)
T cd04710 11 LLKVNDHIYMSSEPPGEPYYIGRIM 35 (135)
T ss_pred EEeCCCEEEEecCCCCCCCEEEEEE
Confidence 4788999999987788999999986
No 59
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=24.24 E-value=92 Score=19.80 Aligned_cols=28 Identities=11% Similarity=0.231 Sum_probs=18.8
Q ss_pred hhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeE
Q 030201 104 VLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHA 142 (181)
Q Consensus 104 i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~ 142 (181)
|.+|+-+|.|-- ++.||.+.|.+. .++.
T Consensus 26 letG~~i~VP~F----------I~~Gd~I~V~T~-~g~Y 53 (56)
T cd05794 26 LETGAEVQVPLF----------IKEGEKIKVDTR-TGEY 53 (56)
T ss_pred ECCCCEEEcCCe----------ecCCCEEEEECC-CCcE
Confidence 346787777764 456899999873 3443
No 60
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=23.76 E-value=2.1e+02 Score=24.41 Aligned_cols=43 Identities=19% Similarity=0.082 Sum_probs=30.7
Q ss_pred ccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeEEEEEEE
Q 030201 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (181)
Q Consensus 91 lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~vaVG~~ 148 (181)
+|.+.+++..+..+++|+.+-.+. .++.+.+.. ++.++|+|..
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 689999999999999999884321 123454543 3479999864
No 61
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A.
Probab=22.94 E-value=2.3e+02 Score=19.84 Aligned_cols=69 Identities=16% Similarity=0.122 Sum_probs=40.3
Q ss_pred CEEEEEEecCCCcchhhhhhhcCC--CCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCCeE
Q 030201 65 NVPLFFNIRDGPYMPTLRLLHQYP--NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHA 142 (181)
Q Consensus 65 g~pl~f~~~~~~~~PTl~~l~~~p--~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~~~ 142 (181)
|..+ -+...+.+.||-.+++.+. ...+.+-+++.-+..-++|-++.... . .+|- |+|+. + +.|
T Consensus 19 Gl~l-g~~~k~~f~Ps~~la~~~~~~~~~~~iel~~e~a~~yl~Ge~i~~~~----------~-~~G~-vlv~~-~-g~~ 83 (102)
T PF13636_consen 19 GLYL-GEIKKNRFEPSHALAMALGPEATKNVIELDDEQALRYLRGEDIELDP----------P-DKGW-VLVTY-E-GFP 83 (102)
T ss_dssp SEEE-EEEETTEEEEBHHHHHCB--GCCS-EEEETCHHHHHHHCT--EE-SS-------------EEE-EEEEE-C-CCE
T ss_pred CcEe-eeEeCCcEEECHHHHHhhCccccceEEECCHHHHHHHHcCCcccCCC----------C-CCcE-EEEEE-C-CEe
Confidence 4433 3445667899998877652 44677888887776667888874433 1 3344 44443 2 678
Q ss_pred EEEEEE
Q 030201 143 LAIGFT 148 (181)
Q Consensus 143 vaVG~~ 148 (181)
+|.|..
T Consensus 84 LG~gk~ 89 (102)
T PF13636_consen 84 LGWGKY 89 (102)
T ss_dssp EEEEEE
T ss_pred eEEEEe
Confidence 888876
No 62
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.94 E-value=1.8e+02 Score=23.56 Aligned_cols=57 Identities=12% Similarity=0.099 Sum_probs=37.7
Q ss_pred hhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 101 IKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 101 ~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~-~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
.+.|..|.-+..--+.. +.-+++||.|.|...+++ ..-+-|+|+-+ +..|..|++..
T Consensus 136 ~r~l~aGq~i~~~~L~~-----p~lV~rG~~V~I~a~~~g~~Vs~~G~AL~~------G~~Ge~IrVrN 193 (214)
T PRK12617 136 RRILPAGSLLSANDLVS-----QRLVRRGDTVPLVSRNGGLEVRMSGRALSD------AGENERVSVEN 193 (214)
T ss_pred eeecCCCCeeCHHHcCC-----cceEcCCCEEEEEEecCCEEEEEEEEEccC------CCCCCEEEEEE
Confidence 34455566555444433 235899999999997765 57778888654 56777776653
No 63
>cd00949 FBP_aldolase_I_bact Fructose-1.6-bisphosphate aldolase found in gram +/- bacteria. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). The enzyme is member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates.
Probab=22.80 E-value=67 Score=27.34 Aligned_cols=37 Identities=32% Similarity=0.474 Sum_probs=30.1
Q ss_pred chhhhhhhcCCCCccEEEECcchhhhhhcCCcccC--Ccc
Q 030201 78 MPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMC--PGL 115 (181)
Q Consensus 78 ~PTl~~l~~~p~~lp~v~v~~~a~~~i~~GAdLm~--pGV 115 (181)
.|++..||....++|-+.||.|+.+. .+|-.+|. ||+
T Consensus 83 ~p~~d~L~e~ggIVPgIKVDKGl~~l-a~Ge~lmk~~~GL 121 (292)
T cd00949 83 KPTADYLWEKKQIVPFLKVDKGLAEE-KNGVQLMKPIPNL 121 (292)
T ss_pred cCHHHHHHhcCCeeeEEEecCCcccC-CCCcccCcCCccH
Confidence 68999999987799999999998754 48888874 554
No 64
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.80 E-value=1.5e+02 Score=23.95 Aligned_cols=56 Identities=9% Similarity=-0.072 Sum_probs=36.5
Q ss_pred hhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 102 KFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 102 ~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~~~~~-~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
+.|..|.-|..--+.. ++-+++||.|.|...+.+ ..-+-|+|+-| +..|..|++..
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 3454555544444332 346899999999986655 57788888654 56777776654
No 65
>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=22.01 E-value=1.2e+02 Score=17.91 Aligned_cols=17 Identities=24% Similarity=0.290 Sum_probs=13.5
Q ss_pred CCCCCCeEEEEeCCCCe
Q 030201 125 EVGAETPVAIMAEGKQH 141 (181)
Q Consensus 125 ~i~~Gd~V~V~~~~~~~ 141 (181)
++++||.|.+...+++.
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 67889999998866553
No 66
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=21.99 E-value=1.5e+02 Score=20.22 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=11.5
Q ss_pred CCCCCCeEEEEeCC
Q 030201 125 EVGAETPVAIMAEG 138 (181)
Q Consensus 125 ~i~~Gd~V~V~~~~ 138 (181)
.+.+||.|.|.+ |
T Consensus 8 ~I~~GD~V~Vi~-G 20 (83)
T CHL00141 8 HVKIGDTVKIIS-G 20 (83)
T ss_pred cccCCCEEEEeE-c
Confidence 689999999988 5
No 67
>COG3526 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]
Probab=20.63 E-value=3.1e+02 Score=19.14 Aligned_cols=50 Identities=16% Similarity=0.318 Sum_probs=30.9
Q ss_pred HHHHHHhHCCCCcchhcccCCCCCcEEEEEeeCceEEEEECCEEEEEEecCCCcchhhhhh
Q 030201 24 IRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLL 84 (181)
Q Consensus 24 Lr~~~~~~f~~~~~~~~~llp~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l 84 (181)
+.+++.++|+. .+.+ +.+.--++.+-.+.+||..+|=+-++|. ||--..|
T Consensus 25 maQElL~TF~~---dlge-------V~L~PgTGG~FeI~~dg~~iWeRKrdGG-FP~ak~L 74 (99)
T COG3526 25 MAQELLSTFAD---DLGE-------VALIPGTGGVFEITCDGVLIWERKRDGG-FPEAKVL 74 (99)
T ss_pred HHHHHHHHHHh---hhhe-------EEEecCCCceEEEEECCEEEEEeeccCC-CCchHHH
Confidence 56778888873 2221 3344335556667889999987666553 6765544
No 68
>PF13144 SAF_2: SAF-like
Probab=20.26 E-value=2.7e+02 Score=21.52 Aligned_cols=40 Identities=13% Similarity=-0.036 Sum_probs=28.4
Q ss_pred CcCCCCCCeEEEEeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030201 123 DEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (181)
Q Consensus 123 ~~~i~~Gd~V~V~~~~~~-~~vaVG~~~~~~~~i~~~~kG~av~~~h 168 (181)
++-+++||.|.|.....+ ..-+-|+|+-+ +..|..|++..
T Consensus 137 ~~~V~~G~~V~v~~~~g~i~i~~~g~Al~~------G~~G~~I~V~N 177 (196)
T PF13144_consen 137 PPLVKRGDIVTVIARSGGISISTEGKALED------GALGDTIRVKN 177 (196)
T ss_pred ceecCCCCEEEEEEEeCCEEEEEEEEEccC------CCCCCEEEEEE
Confidence 357999999999885544 57788888654 56666666543
No 69
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=20.18 E-value=85 Score=25.43 Aligned_cols=28 Identities=14% Similarity=0.260 Sum_probs=21.3
Q ss_pred CCccEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEEe
Q 030201 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMA 136 (181)
Q Consensus 89 ~~lp~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~i~~Gd~V~V~~ 136 (181)
.-||++...|++++++ ++++||+|-|.-
T Consensus 164 ~qLPrI~~~DPvary~--------------------g~k~G~vvkI~R 191 (206)
T PLN03111 164 TQLPRIQVSDPIARYY--------------------GLKRGQVVKIIR 191 (206)
T ss_pred HHCCcccccChhhHhc--------------------CCCCCCEEEEEE
Confidence 4478888888877775 567799998865
Done!