Query psy11162
Match_columns 91
No_of_seqs 101 out of 461
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 19:35:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11162.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11162hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06926 RNAP_II_RPB11 RPB11 su 100.0 4.9E-39 1.1E-43 210.7 11.9 90 2-91 4-93 (93)
2 cd07029 RNAP_I_III_AC19 AC19 s 100.0 9.2E-38 2E-42 201.9 11.1 83 9-91 3-85 (85)
3 PF13656 RNA_pol_L_2: RNA poly 100.0 1.2E-37 2.6E-42 197.9 8.1 77 15-91 1-77 (77)
4 PRK01146 DNA-directed RNA poly 100.0 6.3E-37 1.4E-41 197.9 10.8 83 7-89 3-85 (85)
5 cd06927 RNAP_L L subunit of Ar 100.0 2.3E-36 5.1E-41 194.6 10.7 79 11-89 5-83 (83)
6 cd07027 RNAP_RPB11_like RPB11 100.0 4.3E-36 9.3E-41 193.3 10.5 78 11-88 5-82 (83)
7 COG1761 RPB11 DNA-directed RNA 100.0 3.2E-34 6.9E-39 190.3 11.3 91 1-91 1-91 (99)
8 KOG4392|consensus 100.0 1.4E-33 3E-38 190.4 10.7 89 3-91 17-105 (117)
9 KOG3438|consensus 100.0 6.1E-31 1.3E-35 174.9 8.7 79 13-91 14-92 (105)
10 cd00460 RNAP_RPB11_RPB3 RPB11 99.9 2E-27 4.3E-32 152.9 10.1 76 11-87 5-86 (86)
11 PF01193 RNA_pol_L: RNA polyme 99.7 3.2E-18 6.9E-23 104.9 5.2 65 17-85 1-66 (66)
12 cd07028 RNAP_RPB3_like RPB3 su 96.3 0.017 3.6E-07 42.7 6.5 50 40-90 163-212 (212)
13 PRK14979 DNA-directed RNA poly 96.1 0.03 6.4E-07 41.1 6.8 48 39-90 138-185 (195)
14 cd06928 RNAP_alpha_NTD N-termi 95.9 0.019 4.2E-07 42.2 5.2 45 42-86 164-214 (215)
15 smart00662 RPOLD RNA polymeras 95.8 0.026 5.6E-07 41.6 5.3 34 54-87 191-224 (224)
16 TIGR02027 rpoA DNA-directed RN 95.7 0.047 1E-06 42.1 6.6 48 42-89 155-208 (297)
17 PRK00783 DNA-directed RNA poly 95.4 0.015 3.2E-07 43.6 2.9 34 4-39 2-35 (263)
18 PRK05182 DNA-directed RNA poly 95.2 0.078 1.7E-06 41.2 6.4 48 42-89 172-225 (310)
19 CHL00013 rpoA RNA polymerase a 95.0 0.079 1.7E-06 41.6 6.1 47 42-88 171-222 (327)
20 cd07030 RNAP_D D subunit of Ar 94.8 0.042 9.1E-07 41.0 3.9 36 4-41 2-38 (259)
21 cd06928 RNAP_alpha_NTD N-termi 94.6 0.065 1.4E-06 39.5 4.3 41 10-50 4-49 (215)
22 PRK05182 DNA-directed RNA poly 94.4 0.12 2.6E-06 40.2 5.7 47 4-50 8-59 (310)
23 cd07028 RNAP_RPB3_like RPB3 su 94.4 0.045 9.8E-07 40.4 3.2 33 9-41 5-38 (212)
24 CHL00013 rpoA RNA polymerase a 92.8 0.32 7E-06 38.2 5.6 50 2-51 7-61 (327)
25 cd07031 RNAP_II_RPB3 RPB3 subu 92.5 0.38 8.2E-06 36.5 5.6 37 54-90 225-261 (265)
26 PRK14979 DNA-directed RNA poly 92.4 0.19 4.1E-06 36.9 3.7 43 5-48 4-47 (195)
27 smart00662 RPOLD RNA polymeras 92.1 0.25 5.4E-06 36.4 4.0 33 17-49 2-35 (224)
28 cd07031 RNAP_II_RPB3 RPB3 subu 92.0 0.32 6.8E-06 37.0 4.6 35 12-46 8-43 (265)
29 COG0202 RpoA DNA-directed RNA 91.6 0.28 6.1E-06 38.3 4.0 46 5-50 7-55 (317)
30 cd07030 RNAP_D D subunit of Ar 89.5 1.3 2.7E-05 33.1 5.8 37 54-90 222-258 (259)
31 PRK00783 DNA-directed RNA poly 88.7 1.3 2.7E-05 33.2 5.3 38 53-90 221-258 (263)
32 cd07032 RNAP_I_II_AC40 AC40 su 88.6 1.3 2.9E-05 34.3 5.5 37 53-89 254-290 (291)
33 TIGR02027 rpoA DNA-directed RN 83.7 1.1 2.3E-05 34.7 2.7 29 22-50 11-40 (297)
34 COG2805 PilT Tfp pilus assembl 74.6 2 4.4E-05 34.3 1.7 25 22-46 181-205 (353)
35 cd02071 MM_CoA_mut_B12_BD meth 66.8 17 0.00036 23.9 4.6 27 17-43 3-29 (122)
36 KOG0427|consensus 65.3 19 0.00042 25.5 4.9 49 36-86 74-126 (161)
37 cd04905 ACT_CM-PDT C-terminal 63.8 29 0.00064 20.7 7.0 69 16-86 3-72 (80)
38 COG0202 RpoA DNA-directed RNA 62.4 18 0.00039 28.3 4.7 36 55-90 188-223 (317)
39 PRK02261 methylaspartate mutas 55.8 37 0.00079 23.1 4.9 38 13-50 3-42 (137)
40 cd02067 B12-binding B12 bindin 53.6 37 0.0008 21.7 4.5 27 17-43 3-29 (119)
41 PHA02781 hypothetical protein; 48.4 15 0.00032 23.0 1.8 26 3-28 6-31 (78)
42 cd07032 RNAP_I_II_AC40 AC40 su 47.2 23 0.00051 27.5 3.1 29 11-39 7-35 (291)
43 KOG0758|consensus 46.5 29 0.00064 27.3 3.6 33 45-78 26-61 (297)
44 COG2061 ACT-domain-containing 45.9 94 0.002 22.6 5.8 40 43-86 117-157 (170)
45 TIGR02370 pyl_corrinoid methyl 45.9 77 0.0017 22.6 5.5 40 13-52 84-125 (197)
46 KOG2972|consensus 45.3 71 0.0015 24.9 5.4 51 27-77 93-144 (276)
47 PRK00549 competence damage-ind 44.9 1.2E+02 0.0027 24.2 7.0 54 26-85 191-244 (414)
48 cd02070 corrinoid_protein_B12- 43.6 58 0.0013 23.1 4.5 70 13-82 82-159 (201)
49 KOG1522|consensus 42.4 62 0.0013 25.2 4.7 60 30-89 187-263 (285)
50 PF00403 HMA: Heavy-metal-asso 42.1 63 0.0014 18.1 5.5 46 29-79 13-58 (62)
51 PF03633 Glyco_hydro_65C: Glyc 39.6 22 0.00049 20.1 1.6 24 4-28 29-52 (54)
52 KOG0762|consensus 39.2 26 0.00055 27.5 2.2 26 44-70 24-49 (311)
53 COG2804 PulE Type II secretory 39.2 31 0.00067 28.9 2.8 24 23-46 311-334 (500)
54 PF02482 Ribosomal_S30AE: Sigm 39.2 90 0.002 19.0 4.5 32 58-90 62-93 (97)
55 cd02069 methionine_synthase_B1 36.7 39 0.00084 24.6 2.8 70 13-82 88-165 (213)
56 TIGR01546 GAPDH-II_archae glyc 34.9 1.2E+02 0.0025 24.0 5.4 50 26-78 190-239 (333)
57 cd00552 RaiA RaiA ("ribosome-a 34.8 1.1E+02 0.0023 18.6 4.6 24 66-89 69-92 (93)
58 PF00668 Condensation: Condens 34.7 49 0.0011 23.1 3.0 38 52-90 24-61 (301)
59 PRK04207 glyceraldehyde-3-phos 34.6 2E+02 0.0042 22.4 6.5 51 26-79 193-243 (341)
60 PRK03987 translation initiatio 32.3 1.5E+02 0.0032 22.5 5.4 47 38-87 205-251 (262)
61 PF06657 Cep57_MT_bd: Centroso 31.1 90 0.0019 19.5 3.4 26 65-90 7-32 (79)
62 PHA02243 hypothetical protein 31.0 68 0.0015 22.7 3.1 29 1-34 83-114 (160)
63 PLN02231 alanine transaminase 30.5 2.2E+02 0.0048 23.5 6.5 57 32-91 476-532 (534)
64 PHA02766 hypothetical protein; 30.3 46 0.001 20.5 1.9 49 15-75 15-63 (73)
65 PTZ00377 alanine aminotransfer 30.1 2.2E+02 0.0048 22.7 6.3 57 32-91 424-480 (481)
66 cd07367 CarBb CarBb is the B s 29.3 1E+02 0.0022 23.1 4.0 36 44-86 5-40 (268)
67 PRK10470 ribosome hibernation 29.3 1.5E+02 0.0032 18.4 5.0 32 58-90 60-91 (95)
68 TIGR00741 yfiA ribosomal subun 29.0 1.4E+02 0.003 18.2 5.0 31 59-90 61-91 (95)
69 KOG1521|consensus 28.0 1.5E+02 0.0032 23.8 4.8 44 42-90 293-336 (338)
70 COG5015 Uncharacterized conser 27.8 43 0.00093 23.4 1.6 29 30-63 47-75 (132)
71 KOG1521|consensus 27.6 65 0.0014 25.7 2.8 36 4-39 45-80 (338)
72 COG1058 CinA Predicted nucleot 27.6 2.8E+02 0.0061 21.2 6.8 59 27-88 192-250 (255)
73 PF11470 TUG-UBL1: GLUT4 regul 27.5 1E+02 0.0022 18.7 3.1 23 58-80 8-30 (65)
74 COG3062 NapD Uncharacterized p 26.8 1.9E+02 0.0042 19.1 5.3 44 29-80 20-63 (94)
75 PF00437 T2SE: Type II/IV secr 26.4 1.5E+02 0.0032 21.5 4.4 34 13-46 171-204 (270)
76 TIGR02538 type_IV_pilB type IV 25.3 1.2E+02 0.0026 25.3 4.1 33 14-46 359-392 (564)
77 COG2033 Desulfoferrodoxin [Ene 25.1 52 0.0011 22.9 1.6 11 45-56 57-67 (126)
78 cd04869 ACT_GcvR_2 ACT domains 24.8 1.5E+02 0.0033 17.2 5.5 47 39-85 27-74 (81)
79 COG4115 Uncharacterized protei 24.4 64 0.0014 20.9 1.9 24 30-56 28-51 (84)
80 cd07369 PydA_Rs_like PydA is a 23.7 1.1E+02 0.0024 24.1 3.4 39 44-87 5-45 (329)
81 TIGR00444 mazG MazG family pro 23.6 1.4E+02 0.0029 22.7 3.8 24 66-89 200-223 (248)
82 PF11873 DUF3393: Domain of un 23.6 1.1E+02 0.0024 22.6 3.3 26 54-79 94-119 (204)
83 PRK13358 protocatechuate 4,5-d 23.4 1E+02 0.0022 22.9 3.1 36 44-86 5-40 (269)
84 cd04765 HTH_MlrA-like_sg2 Heli 23.2 1.4E+02 0.003 19.0 3.4 27 65-91 73-99 (99)
85 cd01760 RBD Ubiquitin-like dom 22.7 1.5E+02 0.0032 18.2 3.3 20 60-79 13-32 (72)
86 TIGR00978 asd_EA aspartate-sem 22.1 3.1E+02 0.0067 21.1 5.6 56 23-79 198-262 (341)
87 PF01933 UPF0052: Uncharacteri 22.0 59 0.0013 25.2 1.6 15 23-37 84-98 (300)
88 PRK01215 competence damage-ind 21.8 3E+02 0.0066 20.7 5.4 67 18-87 183-256 (264)
89 PRK09389 (R)-citramalate synth 21.8 4.6E+02 0.0099 21.6 6.9 60 21-82 356-427 (488)
90 PF04263 TPK_catalytic: Thiami 21.8 24 0.00052 23.7 -0.5 14 24-37 98-111 (123)
91 PF08712 Nfu_N: Scaffold prote 21.1 2.3E+02 0.0049 17.8 7.7 68 6-81 13-80 (87)
92 PRK10974 glycerol-3-phosphate 21.0 1.6E+02 0.0035 22.8 3.9 26 64-89 410-435 (438)
93 PF04455 Saccharop_dh_N: LOR/S 20.9 1.8E+02 0.0039 19.2 3.6 38 2-39 34-71 (103)
94 PF02196 RBD: Raf-like Ras-bin 20.9 1.4E+02 0.003 18.0 2.8 21 59-79 13-33 (71)
95 cd07930 bacterial_phosphagen_k 20.7 2.6E+02 0.0057 20.8 4.8 20 59-78 102-122 (232)
96 PF09883 DUF2110: Uncharacteri 20.5 1.5E+02 0.0033 22.4 3.5 35 5-39 31-66 (225)
97 cd00529 RuvC_resolvase Hollida 20.4 2.9E+02 0.0063 18.8 5.1 44 39-82 6-53 (154)
98 PRK09294 acyltransferase PapA5 20.4 1.9E+02 0.0041 22.3 4.2 35 55-90 22-56 (416)
99 cd04880 ACT_AAAH-PDT-like ACT 20.2 1.9E+02 0.0042 16.7 6.4 67 17-85 2-69 (75)
No 1
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=100.00 E-value=4.9e-39 Score=210.68 Aligned_cols=90 Identities=70% Similarity=1.037 Sum_probs=88.1
Q ss_pred ceeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHH
Q psy11162 2 IRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLL 81 (91)
Q Consensus 2 ~~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~ 81 (91)
.+||+++.|++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|.
T Consensus 4 ~~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~~l~ 83 (93)
T cd06926 4 EKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITDLI 83 (93)
T ss_pred ccceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999999999999999999999999999999999999999999998999999999999999
Q ss_pred HHHHHHHhhC
Q psy11162 82 AELSLFEERF 91 (91)
Q Consensus 82 ~~~~~l~~~f 91 (91)
+.|+.++++|
T Consensus 84 ~~~~~~~~~f 93 (93)
T cd06926 84 SELSLLKEEF 93 (93)
T ss_pred HHHHHHHhhC
Confidence 9999999987
No 2
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=100.00 E-value=9.2e-38 Score=201.87 Aligned_cols=83 Identities=37% Similarity=0.539 Sum_probs=80.8
Q ss_pred cCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162 9 LDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE 88 (91)
Q Consensus 9 ~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~ 88 (91)
..++.+|+++|+|.||||||||+||++|+++|+|.||||+||||+++++.|||||+++.+|.+||++|+++|.+.|+++.
T Consensus 3 ~~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (85)
T cd07029 3 GEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHIL 82 (85)
T ss_pred cccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999999999999999999999999999999999999999989999999999999999999999
Q ss_pred hhC
Q psy11162 89 ERF 91 (91)
Q Consensus 89 ~~f 91 (91)
++|
T Consensus 83 ~~f 85 (85)
T cd07029 83 STF 85 (85)
T ss_pred hcC
Confidence 987
No 3
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=100.00 E-value=1.2e-37 Score=197.86 Aligned_cols=77 Identities=52% Similarity=0.817 Sum_probs=72.6
Q ss_pred ceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162 15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF 91 (91)
Q Consensus 15 n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~f 91 (91)
|+++|+|.+|||||||+||++|+++|+|.||||++||||++++.|||||+++.+|.+||++|+++|.++|+.|+++|
T Consensus 1 n~~~f~i~~EDHTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~~F 77 (77)
T PF13656_consen 1 NEITFTIYGEDHTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGITPIEALKKALEDLIKICEELKKEF 77 (77)
T ss_dssp TEEEEEEES--HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 78999999999999999999999999999999999999999999999999998999999999999999999999987
No 4
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=100.00 E-value=6.3e-37 Score=197.95 Aligned_cols=83 Identities=31% Similarity=0.442 Sum_probs=78.7
Q ss_pred eecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 7 KELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 7 ~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
++..++.+|+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|++.|++
T Consensus 3 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~ 82 (85)
T PRK01146 3 IKVLEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDE 82 (85)
T ss_pred EEEEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 44557888999999999999999999999999999999999999999999999999998899999999999999999999
Q ss_pred HHh
Q psy11162 87 FEE 89 (91)
Q Consensus 87 l~~ 89 (91)
|++
T Consensus 83 ~~~ 85 (85)
T PRK01146 83 FLD 85 (85)
T ss_pred HhC
Confidence 864
No 5
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=100.00 E-value=2.3e-36 Score=194.55 Aligned_cols=79 Identities=34% Similarity=0.500 Sum_probs=75.9
Q ss_pred CCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
++.+|+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|++.|+.|.+
T Consensus 5 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~~ 83 (83)
T cd06927 5 EKEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFLD 83 (83)
T ss_pred EcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 5667999999999999999999999999999999999999999999999999999889999999999999999999864
No 6
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=100.00 E-value=4.3e-36 Score=193.33 Aligned_cols=78 Identities=40% Similarity=0.578 Sum_probs=75.0
Q ss_pred CCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162 11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE 88 (91)
Q Consensus 11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~ 88 (91)
++.+|+++|+|.||||||||+||++|+++|+|.||||++|||++++++|||||+++.+|.+||++|+++|.+.|+.|.
T Consensus 5 ~~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l~ 82 (83)
T cd07027 5 SKEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHLG 82 (83)
T ss_pred ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 456699999999999999999999999999999999999999999999999999988999999999999999999986
No 7
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=3.2e-34 Score=190.25 Aligned_cols=91 Identities=36% Similarity=0.565 Sum_probs=87.3
Q ss_pred CceeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHH
Q psy11162 1 MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL 80 (91)
Q Consensus 1 ~~~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l 80 (91)
|-+++.+...++.+|+++|++.||||||||+|+++|+++|+|.||||+||||+.+++.+||||+++++|.+||++|++.+
T Consensus 1 ~~~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i 80 (99)
T COG1761 1 MTPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKI 80 (99)
T ss_pred CCCceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHH
Confidence 55788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhC
Q psy11162 81 LAELSLFEERF 91 (91)
Q Consensus 81 ~~~~~~l~~~f 91 (91)
++.|++|.++|
T Consensus 81 ~~~~~~l~~~~ 91 (99)
T COG1761 81 LKDLEELLDQF 91 (99)
T ss_pred HHHHHHHHHHH
Confidence 99999999843
No 8
>KOG4392|consensus
Probab=100.00 E-value=1.4e-33 Score=190.40 Aligned_cols=89 Identities=72% Similarity=1.110 Sum_probs=86.8
Q ss_pred eeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162 3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLA 82 (91)
Q Consensus 3 ~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~ 82 (91)
+||++..|+|++|++.|+|++|||||||+||.+|++||+|.||||++|||+..++.|||||..+++|.+|+..|+.++..
T Consensus 17 kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d~~p~~al~~a~~~l~~ 96 (117)
T KOG4392|consen 17 KKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTEDCSPADALTNAITDLIE 96 (117)
T ss_pred ceeEEecCCCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCCCCHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhC
Q psy11162 83 ELSLFEERF 91 (91)
Q Consensus 83 ~~~~l~~~f 91 (91)
..+.++..|
T Consensus 97 el~~l~~~f 105 (117)
T KOG4392|consen 97 ELSLLENRF 105 (117)
T ss_pred HHHHHHHHH
Confidence 999998765
No 9
>KOG3438|consensus
Probab=99.97 E-value=6.1e-31 Score=174.91 Aligned_cols=79 Identities=35% Similarity=0.616 Sum_probs=76.4
Q ss_pred CCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162 13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF 91 (91)
Q Consensus 13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~f 91 (91)
..++.+|++..|||||||+||+.|+++|.|+||||.||||+++++.|||||.++..+.++|++|+++|.+.|+.+.++|
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF 92 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKF 92 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999999999999999999999999999999999999999888999999999999999999999876
No 10
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=99.95 E-value=2e-27 Score=152.95 Aligned_cols=76 Identities=45% Similarity=0.628 Sum_probs=72.4
Q ss_pred CCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCC------CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q psy11162 11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPL------EHKFILRIQTTAESTPHDALMNAITDLLAEL 84 (91)
Q Consensus 11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl------~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~ 84 (91)
++.+|+++|+|.||||||||+||++|++ +.|.||||+||||+ .+++.|+|+|+|+.+|.+||++|++.|.+.|
T Consensus 5 ~~~~~~~~~~~~~edhTl~n~L~~~l~~-~pV~~a~Y~v~hp~~~~~~~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~ 83 (86)
T cd00460 5 EKEKNYVDFVLENEDHTLGNSLRRILLK-SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKL 83 (86)
T ss_pred cCCCCEEEEEEeCCCchHHHHHHHHHhC-CCceEEEEEeCCCccCCCCCCCeEEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence 4566999999999999999999999999 99999999999999 9999999999999999999999999999998
Q ss_pred HHH
Q psy11162 85 SLF 87 (91)
Q Consensus 85 ~~l 87 (91)
+.|
T Consensus 84 ~~~ 86 (86)
T cd00460 84 EHL 86 (86)
T ss_pred hhC
Confidence 764
No 11
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=99.74 E-value=3.2e-18 Score=104.91 Aligned_cols=65 Identities=46% Similarity=0.729 Sum_probs=61.4
Q ss_pred EEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy11162 17 AIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELS 85 (91)
Q Consensus 17 ~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~ 85 (91)
++|.+.|+|||+||+||..|+++ |.|.+++ ||..+++.++|+|+|+.+|.++|.+|++.|.+.|+
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~ 66 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLTPKEALLKAIKILKEKLN 66 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence 57999999999999999999999 9999999 99999999999999999999999999999998874
No 12
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=96.32 E-value=0.017 Score=42.71 Aligned_cols=50 Identities=14% Similarity=0.313 Sum_probs=42.3
Q ss_pred CCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 40 PHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 40 ~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.=|.-|.|++. |-.+...|.|.|+|..+|.+|+.+|++-|.+.+++|.++
T Consensus 163 sPV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~~ 212 (212)
T cd07028 163 GPVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILLA 212 (212)
T ss_pred CCceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhhC
Confidence 33566778854 356889999999999999999999999999999998763
No 13
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=96.09 E-value=0.03 Score=41.13 Aligned_cols=48 Identities=21% Similarity=0.280 Sum_probs=39.6
Q ss_pred CCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 39 DPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 39 ~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.| |. |.|+..- .++..|.|.|+|+.+|.+|+..|++-|.+.++.|.+.
T Consensus 138 ~p-vd-a~y~~~~--~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~ 185 (195)
T PRK14979 138 QP-CN-AVYKQIS--NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQE 185 (195)
T ss_pred cc-ee-eEEecCC--CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45 44 5565332 4899999999999999999999999999999998764
No 14
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=95.93 E-value=0.019 Score=42.24 Aligned_cols=45 Identities=29% Similarity=0.298 Sum_probs=36.9
Q ss_pred eeeeeeeCCC------CCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 42 VLFAGYKQPH------PLEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 42 V~fAgY~vpH------Pl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
|.-+.|.|.- .-.+...|.|.|+|+.+|.+||..|++.|.+.+..
T Consensus 164 V~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~~ 214 (215)
T cd06928 164 VRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSP 214 (215)
T ss_pred eEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhhc
Confidence 6666777543 23567899999999999999999999999988753
No 15
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=95.76 E-value=0.026 Score=41.64 Aligned_cols=34 Identities=26% Similarity=0.439 Sum_probs=30.9
Q ss_pred CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q psy11162 54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLF 87 (91)
Q Consensus 54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l 87 (91)
.++..|.|.|+|..+|.+||.+|++-|.+.++.|
T Consensus 191 ~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~~ 224 (224)
T smart00662 191 YDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224 (224)
T ss_pred CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhhC
Confidence 5789999999999999999999999999988753
No 16
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=95.67 E-value=0.047 Score=42.10 Aligned_cols=48 Identities=33% Similarity=0.429 Sum_probs=39.1
Q ss_pred eeeeeeeCCC------CCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 42 VLFAGYKQPH------PLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 42 V~fAgY~vpH------Pl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
|.-+.|.+.. ...+...|.|.|+|..+|.+|+.+|++-|.+.|..|.+
T Consensus 155 V~~Vny~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 155 VLKVNYEVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred eEEEEEEEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 4556677653 23467999999999999999999999999999987753
No 17
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=95.38 E-value=0.015 Score=43.56 Aligned_cols=34 Identities=24% Similarity=0.233 Sum_probs=28.0
Q ss_pred eeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC
Q psy11162 4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD 39 (91)
Q Consensus 4 kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~ 39 (91)
++.+...+ ++.++|.+.|-|+|+||+||-.|+.+
T Consensus 2 ~~~~~~~~--~~~~~f~~~g~~~t~~NalRRvlls~ 35 (263)
T PRK00783 2 EIEILELD--DRSARFVVEGVTPAFANAIRRAMIAD 35 (263)
T ss_pred ceEEEEcC--CcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence 34454444 48899999999999999999999986
No 18
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=95.17 E-value=0.078 Score=41.18 Aligned_cols=48 Identities=31% Similarity=0.392 Sum_probs=39.4
Q ss_pred eeeeeeeCCCC------CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 42 VLFAGYKQPHP------LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 42 V~fAgY~vpHP------l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
|.-+.|.+.-. -.+...|.|.|+|+.+|.+||.+|++-|.+.+..|.+
T Consensus 172 V~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~ 225 (310)
T PRK05182 172 VKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD 225 (310)
T ss_pred ccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 56677776542 1467999999999999999999999999999987754
No 19
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=95.01 E-value=0.079 Score=41.59 Aligned_cols=47 Identities=26% Similarity=0.260 Sum_probs=39.3
Q ss_pred eeeeeeeCCCC-----CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162 42 VLFAGYKQPHP-----LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE 88 (91)
Q Consensus 42 V~fAgY~vpHP-----l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~ 88 (91)
|.-+.|.|..- -.+...|-|.|+|+++|.+||..|++-|.+.+.-|.
T Consensus 171 V~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~ 222 (327)
T CHL00013 171 VRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFL 222 (327)
T ss_pred eeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 66677777651 257899999999999999999999999999987764
No 20
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=94.78 E-value=0.042 Score=41.01 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=28.8
Q ss_pred eeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC-CC
Q psy11162 4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PH 41 (91)
Q Consensus 4 kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~ 41 (91)
+|++...+ ++.+.|.+.|-|+|+||+||-.|+.. |.
T Consensus 2 ~~~~~~~~--~~~~~f~~~g~~~s~~NalRRills~vp~ 38 (259)
T cd07030 2 EIEVLELD--DDRARFVLEGVPPAFANAIRRAIISEVPT 38 (259)
T ss_pred ceEEEecC--CCEEEEEEeCCCHHHHHHHHHHHHhcCCe
Confidence 34554444 48999999999999999999999986 44
No 21
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=94.55 E-value=0.065 Score=39.45 Aligned_cols=41 Identities=29% Similarity=0.427 Sum_probs=32.2
Q ss_pred CCCCCceEEEEE----ecCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162 10 DTKVPNAAIFTV----NKEDHTLGNMIRNQLLKD-PHVLFAGYKQP 50 (91)
Q Consensus 10 ~~k~~n~~~~~i----~~EdHTlgNlLr~~L~~~-~~V~fAgY~vp 50 (91)
++..++.+.|.+ .|.++|+||+||..|+.+ |+...-+-++.
T Consensus 4 ~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~ 49 (215)
T cd06928 4 ENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE 49 (215)
T ss_pred ccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence 445579999999 789999999999999885 66655555544
No 22
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=94.39 E-value=0.12 Score=40.16 Aligned_cols=47 Identities=30% Similarity=0.333 Sum_probs=35.6
Q ss_pred eeeeecCCCCCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162 4 KIIKELDTKVPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAGYKQP 50 (91)
Q Consensus 4 kv~~~~~~k~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAgY~vp 50 (91)
++.+...+..++.+.|.+. |.++|+||+||-.|+.+ |+...-+-++.
T Consensus 8 ~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~ 59 (310)
T PRK05182 8 KIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID 59 (310)
T ss_pred EEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc
Confidence 4555543334799999997 99999999999999885 76666666654
No 23
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=94.38 E-value=0.045 Score=40.41 Aligned_cols=33 Identities=15% Similarity=0.346 Sum_probs=28.1
Q ss_pred cCCCCCceEEEEEecCCcchHHHHHHHHhcC-CC
Q psy11162 9 LDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PH 41 (91)
Q Consensus 9 ~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~ 41 (91)
.-++.++.+.|.+.|-|+|+||+||-.|+.. |.
T Consensus 5 i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~ 38 (212)
T cd07028 5 IREADKDNVDFILSGVDLAMANALRRVMIAEVPT 38 (212)
T ss_pred EEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcc
Confidence 3456668999999999999999999999986 44
No 24
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=92.75 E-value=0.32 Score=38.18 Aligned_cols=50 Identities=18% Similarity=0.203 Sum_probs=40.8
Q ss_pred ceeeeeecCCCCCceEEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeeeCCC
Q psy11162 2 IRKIIKELDTKVPNAAIFTVN----KEDHTLGNMIRNQLLKD-PHVLFAGYKQPH 51 (91)
Q Consensus 2 ~~kv~~~~~~k~~n~~~~~i~----~EdHTlgNlLr~~L~~~-~~V~fAgY~vpH 51 (91)
++-+....++...+++.|.|. |..|||||+||..|+.+ |+..+.+-++.+
T Consensus 7 ~~~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 7 WKCVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred ccceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 455777788888999999996 57779999999999985 887777777654
No 25
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=92.51 E-value=0.38 Score=36.54 Aligned_cols=37 Identities=16% Similarity=0.345 Sum_probs=34.0
Q ss_pred CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.+.+.|.|.|.|..+|.++|.+|++-|.+.++.|.+.
T Consensus 225 ~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~ 261 (265)
T cd07031 225 PDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQ 261 (265)
T ss_pred CCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999998764
No 26
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=92.39 E-value=0.19 Score=36.92 Aligned_cols=43 Identities=12% Similarity=0.273 Sum_probs=33.3
Q ss_pred eeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC-CCeeeeeee
Q psy11162 5 IIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYK 48 (91)
Q Consensus 5 v~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~ 48 (91)
+.++.-++..+.+.|.+. -|.|+||+||-.|+.. |+...-+-+
T Consensus 4 ~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~ 47 (195)
T PRK14979 4 IKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVY 47 (195)
T ss_pred cceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEE
Confidence 345556778899999999 9999999999999985 654444433
No 27
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=92.05 E-value=0.25 Score=36.43 Aligned_cols=33 Identities=27% Similarity=0.351 Sum_probs=26.2
Q ss_pred EEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeC
Q psy11162 17 AIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQ 49 (91)
Q Consensus 17 ~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~v 49 (91)
+.|.+.+-++|+||+||-.|+.. |....-+.++
T Consensus 2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I 35 (224)
T smart00662 2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI 35 (224)
T ss_pred eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence 67999999999999999999985 6555444443
No 28
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=92.04 E-value=0.32 Score=36.96 Aligned_cols=35 Identities=14% Similarity=0.327 Sum_probs=28.1
Q ss_pred CCCceEEEEEecCCcchHHHHHHHHhcC-CCeeeee
Q psy11162 12 KVPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAG 46 (91)
Q Consensus 12 k~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAg 46 (91)
..++.++|.+.+=|+|+||+||-.|+.. |....-.
T Consensus 8 ~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~ 43 (265)
T cd07031 8 LTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDL 43 (265)
T ss_pred cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEE
Confidence 4458999999999999999999999885 5543333
No 29
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=91.58 E-value=0.28 Score=38.32 Aligned_cols=46 Identities=20% Similarity=0.089 Sum_probs=33.3
Q ss_pred eeeecCCC--CCceEEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162 5 IIKELDTK--VPNAAIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQP 50 (91)
Q Consensus 5 v~~~~~~k--~~n~~~~~i~~EdHTlgNlLr~~L~~~-~~V~fAgY~vp 50 (91)
|++...++ .+-.+++...|-+|||||+||-.|+.. |....-+-++.
T Consensus 7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~ 55 (317)
T COG0202 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEID 55 (317)
T ss_pred eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEe
Confidence 44444443 478899999999999999999999885 66544443333
No 30
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=89.50 E-value=1.3 Score=33.09 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=33.3
Q ss_pred CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 54 EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 54 ~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.+...+.|.|.|..+|.+++++|++-|.+.++.|.++
T Consensus 222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~ 258 (259)
T cd07030 222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258 (259)
T ss_pred CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4557789999999999999999999999999999765
No 31
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=88.73 E-value=1.3 Score=33.16 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=34.2
Q ss_pred CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 53 LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 53 l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
..+...+.+.|.|..+|.++++.|++-|.+.+++|.+.
T Consensus 221 ~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~ 258 (263)
T PRK00783 221 DENKFIFTVESDGSLPVEEILLEALKILKRKADELIEA 258 (263)
T ss_pred cCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999999999999999999998764
No 32
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=88.62 E-value=1.3 Score=34.28 Aligned_cols=37 Identities=24% Similarity=0.349 Sum_probs=33.8
Q ss_pred CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 53 LEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 53 l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
-.+.+.+.|.+.|..+|.+.+.+|++-|.+.|+.|.+
T Consensus 254 ~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~ 290 (291)
T cd07032 254 VRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred eCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 3566999999999999999999999999999999876
No 33
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=83.73 E-value=1.1 Score=34.68 Aligned_cols=29 Identities=31% Similarity=0.358 Sum_probs=23.1
Q ss_pred ecCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q psy11162 22 NKEDHTLGNMIRNQLLKD-PHVLFAGYKQP 50 (91)
Q Consensus 22 ~~EdHTlgNlLr~~L~~~-~~V~fAgY~vp 50 (91)
.|.+||+||+||-.|+.+ |++...+-++.
T Consensus 11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~ 40 (297)
T TIGR02027 11 RGFGITLGNALRRVLLSSIPGAAITAVKID 40 (297)
T ss_pred CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence 478999999999999985 77766665554
No 34
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=74.62 E-value=2 Score=34.31 Aligned_cols=25 Identities=28% Similarity=0.648 Sum_probs=22.4
Q ss_pred ecCCcchHHHHHHHHhcCCCeeeee
Q psy11162 22 NKEDHTLGNMIRNQLLKDPHVLFAG 46 (91)
Q Consensus 22 ~~EdHTlgNlLr~~L~~~~~V~fAg 46 (91)
..-.|++.|+||..|-+||+|.+.|
T Consensus 181 G~dT~sF~~aLraALReDPDVIlvG 205 (353)
T COG2805 181 GRDTLSFANALRAALREDPDVILVG 205 (353)
T ss_pred cccHHHHHHHHHHHhhcCCCEEEEe
Confidence 3456899999999999999999998
No 35
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=66.81 E-value=17 Score=23.87 Aligned_cols=27 Identities=15% Similarity=0.199 Sum_probs=23.3
Q ss_pred EEEEEecCCcchHHHHHHHHhcCCCee
Q psy11162 17 AIFTVNKEDHTLGNMIRNQLLKDPHVL 43 (91)
Q Consensus 17 ~~~~i~~EdHTlgNlLr~~L~~~~~V~ 43 (91)
+..++.+|.|++|..+-..+++..+.+
T Consensus 3 v~~~~~gd~H~lG~~~~~~~l~~~G~~ 29 (122)
T cd02071 3 LVAKPGLDGHDRGAKVIARALRDAGFE 29 (122)
T ss_pred EEEecCCChhHHHHHHHHHHHHHCCCE
Confidence 567889999999999999999987644
No 36
>KOG0427|consensus
Probab=65.26 E-value=19 Score=25.52 Aligned_cols=49 Identities=27% Similarity=0.443 Sum_probs=39.3
Q ss_pred HhcCCCeeeeeeeCC-CC---CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 36 LLKDPHVLFAGYKQP-HP---LEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 36 L~~~~~V~fAgY~vp-HP---l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
=+..|+|.|.|= +| || ..+-|-|.|-+++ -+|.-.+...|-+|++++..
T Consensus 74 P~esPqVmF~~~-~P~HPHiYSNGHICL~iL~d~-WsPAmsv~SvClSIlSMLSS 126 (161)
T KOG0427|consen 74 PMESPQVMFVGP-APLHPHIYSNGHICLDILYDS-WSPAMSVQSVCLSILSMLSS 126 (161)
T ss_pred CCCCCeEEEecC-CCCCCceecCCeEEEEeeccc-CCcchhhHHHHHHHHHHHcc
Confidence 356799999998 55 88 3577888898875 48988899999998888754
No 37
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=63.76 E-value=29 Score=20.74 Aligned_cols=69 Identities=10% Similarity=0.123 Sum_probs=38.3
Q ss_pred eEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCC-CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 16 AAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHP-LEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 16 ~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHP-l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
++.|++.++-=+|..+|...-..+=++.-- -..|++ -.....++|++++..+ .+.+++++++|...+..
T Consensus 3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i-~s~p~~~~~~~~~f~vd~~~~~~-~~~~~~~l~~l~~~~~~ 72 (80)
T cd04905 3 SIVFTLPNKPGALYDVLGVFAERGINLTKI-ESRPSKGGLWEYVFFIDFEGHIE-DPNVAEALEELKRLTEF 72 (80)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCcCEEEE-EEEEcCCCCceEEEEEEEECCCC-CHHHHHHHHHHHHhCCe
Confidence 455666554444444444333333333222 233443 2456889999886533 37788888888776543
No 38
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=62.39 E-value=18 Score=28.35 Aligned_cols=36 Identities=25% Similarity=0.303 Sum_probs=31.5
Q ss_pred CeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 55 HKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 55 ~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
+...+.+-|+|++.|.+|+..|.+-+.+.|+.+.+.
T Consensus 188 Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~ 223 (317)
T COG0202 188 DHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVEL 223 (317)
T ss_pred eeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhh
Confidence 456777889999999999999999999999988764
No 39
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=55.81 E-value=37 Score=23.10 Aligned_cols=38 Identities=18% Similarity=0.286 Sum_probs=29.1
Q ss_pred CCceEEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCC
Q psy11162 13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPH--VLFAGYKQP 50 (91)
Q Consensus 13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~--V~fAgY~vp 50 (91)
.+.-+..++.+|.|++|..+-..+++..+ |.+-|.++|
T Consensus 3 ~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp 42 (137)
T PRK02261 3 KKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTS 42 (137)
T ss_pred CCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCC
Confidence 34567889999999999999999999865 444444444
No 40
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=53.64 E-value=37 Score=21.68 Aligned_cols=27 Identities=30% Similarity=0.414 Sum_probs=22.6
Q ss_pred EEEEEecCCcchHHHHHHHHhcCCCee
Q psy11162 17 AIFTVNKEDHTLGNMIRNQLLKDPHVL 43 (91)
Q Consensus 17 ~~~~i~~EdHTlgNlLr~~L~~~~~V~ 43 (91)
+.....+|.|++|..+-..+++..+.+
T Consensus 3 l~~~~~~e~H~lG~~~~~~~l~~~G~~ 29 (119)
T cd02067 3 VIATVGGDGHDIGKNIVARALRDAGFE 29 (119)
T ss_pred EEEeeCCchhhHHHHHHHHHHHHCCCE
Confidence 456789999999999999999876544
No 41
>PHA02781 hypothetical protein; Provisional
Probab=48.43 E-value=15 Score=23.01 Aligned_cols=26 Identities=31% Similarity=0.373 Sum_probs=22.4
Q ss_pred eeeeeecCCCCCceEEEEEecCCcch
Q psy11162 3 RKIIKELDTKVPNAAIFTVNKEDHTL 28 (91)
Q Consensus 3 ~kv~~~~~~k~~n~~~~~i~~EdHTl 28 (91)
.|+.++.|+|..|..++...-|.-|+
T Consensus 6 dkikitvdskignvvtisynlekiti 31 (78)
T PHA02781 6 DKIKITVDSKIGNVVTISYNLEKITI 31 (78)
T ss_pred ceEEEEeecccCcEEEEEeeeEEEEE
Confidence 58999999999999999888777665
No 42
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=47.16 E-value=23 Score=27.45 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=25.4
Q ss_pred CCCCceEEEEEecCCcchHHHHHHHHhcC
Q psy11162 11 TKVPNAAIFTVNKEDHTLGNMIRNQLLKD 39 (91)
Q Consensus 11 ~k~~n~~~~~i~~EdHTlgNlLr~~L~~~ 39 (91)
+..++.++|.+.|-|=.+.|+||-.++..
T Consensus 7 ~~~~~~~~f~l~~~d~s~ANAlRRimiaE 35 (291)
T cd07032 7 SLSDEELEFDLIGVDASIANAFRRILLAE 35 (291)
T ss_pred ECCCCEEEEEEecCCHHHHHHHHHHHHhc
Confidence 34558999999999999999999998875
No 43
>KOG0758|consensus
Probab=46.50 E-value=29 Score=27.27 Aligned_cols=33 Identities=21% Similarity=0.323 Sum_probs=23.5
Q ss_pred eeeeCCCCCCCeeEEEEEeCCCCC---HHHHHHHHHH
Q psy11162 45 AGYKQPHPLEHKFILRIQTTAEST---PHDALMNAIT 78 (91)
Q Consensus 45 AgY~vpHPl~~~~~l~Iqt~~~~~---p~~al~~a~~ 78 (91)
|+--|-||+ +.+.+|+||-.... .++++++.++
T Consensus 26 ~~vlVGhPf-DTvKVRlQt~~~~~y~~~~~c~~~t~~ 61 (297)
T KOG0758|consen 26 AQVLVGHPF-DTVKVRLQTQNTPVYKGTLDCVKKTLK 61 (297)
T ss_pred hhhhccCCc-cceEEeeeccCCCCcccHHHHHHHHHH
Confidence 566789999 56999999965422 4666666654
No 44
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=45.87 E-value=94 Score=22.57 Aligned_cols=40 Identities=15% Similarity=0.037 Sum_probs=29.9
Q ss_pred eeeeeeCCCC-CCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 43 LFAGYKQPHP-LEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 43 ~fAgY~vpHP-l~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
.--.-+|||| .+....++|...+. +.+++|++.+.+.|.+
T Consensus 117 vDl~L~Mp~~e~~SsA~iti~a~~~----e~l~ea~~~l~ev~~e 157 (170)
T COG2061 117 VDLSLSMPGIEGESSARITIIAVGK----EKLDEALRRLKEVAME 157 (170)
T ss_pred EEEEeecCCCCCCcceeEEEEEcCh----hHHHHHHHHHHHHHhh
Confidence 3345789999 47778889887553 7888888888877653
No 45
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=45.87 E-value=77 Score=22.59 Aligned_cols=40 Identities=18% Similarity=0.204 Sum_probs=31.6
Q ss_pred CCceEEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCCCC
Q psy11162 13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPH--VLFAGYKQPHP 52 (91)
Q Consensus 13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~--V~fAgY~vpHP 52 (91)
.+..+-.++.||.|.||..+...+++..+ |.+.|-++|-.
T Consensus 84 ~~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e 125 (197)
T TIGR02370 84 LGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPID 125 (197)
T ss_pred CCeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHH
Confidence 35678899999999999999999999864 55566666643
No 46
>KOG2972|consensus
Probab=45.29 E-value=71 Score=24.87 Aligned_cols=51 Identities=18% Similarity=0.202 Sum_probs=37.5
Q ss_pred chHHHHHHHHhc-CCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHH
Q psy11162 27 TLGNMIRNQLLK-DPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAI 77 (91)
Q Consensus 27 TlgNlLr~~L~~-~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~ 77 (91)
++-|.|+...-+ .+.|.|+-|.+-||.-=-+.+..-|+.......+++.++
T Consensus 93 ~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~ 144 (276)
T KOG2972|consen 93 GIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIF 144 (276)
T ss_pred HHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHH
Confidence 577888888775 589999999999999877888888875433334444443
No 47
>PRK00549 competence damage-inducible protein A; Provisional
Probab=44.89 E-value=1.2e+02 Score=24.24 Aligned_cols=54 Identities=19% Similarity=0.306 Sum_probs=33.9
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy11162 26 HTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELS 85 (91)
Q Consensus 26 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~ 85 (91)
=.|...|...+...++|.++-| |+ ...+.+|+...+. +. +..++.++.+.+.+.
T Consensus 191 s~l~~~L~~l~~~~~~v~ig~~--~~--~~~~~vrl~~~~~-~~-~~~~~~~~~~~~~i~ 244 (414)
T PRK00549 191 SQLATTLRDLIDNQTNPTIAPY--AK--DGEVTLRLTAKAR-SE-EEAEKLIDPLEEEIR 244 (414)
T ss_pred HHHHHHHHHHHhcCCCCEEEEC--cc--CCEEEEEEEEecC-CH-HHHHHHHHHHHHHHH
Confidence 4677888777778899998866 33 3567888876653 33 333444444444433
No 48
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=43.60 E-value=58 Score=23.12 Aligned_cols=70 Identities=21% Similarity=0.185 Sum_probs=42.9
Q ss_pred CCceEEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCCCCC------CCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162 13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPH--VLFAGYKQPHPL------EHKFILRIQTTAESTPHDALMNAITDLLA 82 (91)
Q Consensus 13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~--V~fAgY~vpHPl------~~~~~l~Iqt~~~~~p~~al~~a~~~l~~ 82 (91)
.+..+..++.||.|+||-.+...+++..+ |.+.|-++|+.- +.++.+---+.........+++.++.|.+
T Consensus 82 ~~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~~~d~v~lS~~~~~~~~~~~~~i~~lr~ 159 (201)
T cd02070 82 KGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEALKE 159 (201)
T ss_pred CCeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHH
Confidence 34667889999999999999999888765 445566666542 23333322222112334556666655544
No 49
>KOG1522|consensus
Probab=42.36 E-value=62 Score=25.21 Aligned_cols=60 Identities=18% Similarity=0.313 Sum_probs=45.4
Q ss_pred HHHHHHHh--------cCCCeeeeeeeCC----CCC-----CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 30 NMIRNQLL--------KDPHVLFAGYKQP----HPL-----EHKFILRIQTTAESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 30 NlLr~~L~--------~~~~V~fAgY~vp----HPl-----~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
|.||+.+. +-|..+.+++.-+ -|. -+++.+.|...|+..|..++..|++-|.+.++.|..
T Consensus 187 n~lrhT~y~~e~~~~~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~ 263 (285)
T KOG1522|consen 187 NKLRHTLYWFEEDDLIEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRL 263 (285)
T ss_pred HhhhccCCCccccchhhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66666554 4466777777655 121 167899999999999999999999999999888764
No 50
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=42.12 E-value=63 Score=18.07 Aligned_cols=46 Identities=15% Similarity=0.192 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHH
Q psy11162 29 GNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITD 79 (91)
Q Consensus 29 gNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~ 79 (91)
.+.++..|.+.|+|.-+-....- +.+. |..+......+.+.+++++
T Consensus 13 ~~~v~~~l~~~~GV~~v~vd~~~---~~v~--v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 13 AKKVEKALSKLPGVKSVKVDLET---KTVT--VTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp HHHHHHHHHTSTTEEEEEEETTT---TEEE--EEESTTTSCHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCcEEEEECCC---CEEE--EEEecCCCCHHHHHHHHHH
Confidence 46788999999999766655432 4444 4444332233777777765
No 51
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=39.61 E-value=22 Score=20.06 Aligned_cols=24 Identities=25% Similarity=0.174 Sum_probs=11.8
Q ss_pred eeeeecCCCCCceEEEEEecCCcch
Q psy11162 4 KIIKELDTKVPNAAIFTVNKEDHTL 28 (91)
Q Consensus 4 kv~~~~~~k~~n~~~~~i~~EdHTl 28 (91)
++++...+.. ..+++.+.|+.+||
T Consensus 29 ~v~v~~~~g~-~~l~i~v~g~~~~L 52 (54)
T PF03633_consen 29 KVTVTLLSGD-APLTIKVYGEEVTL 52 (54)
T ss_dssp EEEEEEEESS---EEEEETT-----
T ss_pred EEEEEEccCC-ccEEEEECCCcccc
Confidence 4556655554 67888899988886
No 52
>KOG0762|consensus
Probab=39.19 E-value=26 Score=27.45 Aligned_cols=26 Identities=35% Similarity=0.579 Sum_probs=20.8
Q ss_pred eeeeeCCCCCCCeeEEEEEeCCCCCHH
Q psy11162 44 FAGYKQPHPLEHKFILRIQTTAESTPH 70 (91)
Q Consensus 44 fAgY~vpHPl~~~~~l~Iqt~~~~~p~ 70 (91)
.||--+-||+ +.+.+|.||.++.+|.
T Consensus 24 vAGVl~GhPl-DTvkVrlQtqs~~~Pq 49 (311)
T KOG0762|consen 24 VAGVLVGHPL-DTVKVRLQTQSSKSPQ 49 (311)
T ss_pred cceeeecCCc-ceeEEEEeccCCCCCc
Confidence 3788899999 5689999998766653
No 53
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=39.16 E-value=31 Score=28.95 Aligned_cols=24 Identities=33% Similarity=0.544 Sum_probs=22.2
Q ss_pred cCCcchHHHHHHHHhcCCCeeeee
Q psy11162 23 KEDHTLGNMIRNQLLKDPHVLFAG 46 (91)
Q Consensus 23 ~EdHTlgNlLr~~L~~~~~V~fAg 46 (91)
+-+-|+.++||..|-+||+|.+.|
T Consensus 311 k~gltfa~~LRa~LRqDPDvImVG 334 (500)
T COG2804 311 KIGLTFARALRAILRQDPDVIMVG 334 (500)
T ss_pred ccCCCHHHHHHHHhccCCCeEEEe
Confidence 457899999999999999999988
No 54
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 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 family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=39.16 E-value=90 Score=19.00 Aligned_cols=32 Identities=22% Similarity=0.302 Sum_probs=24.2
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 58 ILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 58 ~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.+++...+ .+...|+..|++.|...+....++
T Consensus 62 ~l~a~~~~-~d~~~Aid~a~dkl~rql~k~k~k 93 (97)
T PF02482_consen 62 VLVAEESA-EDLYAAIDEAFDKLERQLRKYKEK 93 (97)
T ss_dssp EEEEEEEE-SSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred eEEEEEec-CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444443 489999999999999998877654
No 55
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=36.67 E-value=39 Score=24.64 Aligned_cols=70 Identities=17% Similarity=0.170 Sum_probs=43.6
Q ss_pred CCceEEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCCCCC------CCeeEEEEEeCCCCCHHHHHHHHHHHHHH
Q psy11162 13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPH--VLFAGYKQPHPL------EHKFILRIQTTAESTPHDALMNAITDLLA 82 (91)
Q Consensus 13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~--V~fAgY~vpHPl------~~~~~l~Iqt~~~~~p~~al~~a~~~l~~ 82 (91)
.+..+..++.||.|.||-.+...+++..+ |.+-|-++|-+- +.++.+..-+....+....+++.++.|.+
T Consensus 88 ~~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~~~~~V~lS~~~~~~~~~~~~~i~~L~~ 165 (213)
T cd02069 88 KGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIEKILEAAKEHKADIIGLSGLLVPSLDEMVEVAEEMNR 165 (213)
T ss_pred CCeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEccchhccHHHHHHHHHHHHh
Confidence 45678889999999999999999999864 555665565432 23343332222222344555665555543
No 56
>TIGR01546 GAPDH-II_archae glyceraldehyde-3-phosphate dehydrogenase, type II. All of the members of the seed are characterized. See, for instance. This model is very solid, there are no species falling between trusted and noise at this time. The closest relatives scoring in the noise are the class I GAPDH's.
Probab=34.93 E-value=1.2e+02 Score=23.98 Aligned_cols=50 Identities=14% Similarity=0.258 Sum_probs=39.6
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHH
Q psy11162 26 HTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAIT 78 (91)
Q Consensus 26 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~ 78 (91)
|| +-.+...|=... +.=.+.+||.|+.+-.-+.+++++..+. +-+.++++
T Consensus 190 ~~-a~av~~VlP~L~-i~g~AvrVPt~~vs~~dl~v~l~~~~t~-eeV~~~l~ 239 (333)
T TIGR01546 190 HH-GPDVQTVIPNLN-IETMAFVVPTTLMHVHSIMVELKKPVTK-DDIIDILE 239 (333)
T ss_pred ch-HHHHHHcCCCCC-ccEEEEEeCCCCcEEEEEEEEECCCCCH-HHHHHHHH
Confidence 77 888888887766 8888999999999999999999887654 44444543
No 57
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=34.78 E-value=1.1e+02 Score=18.59 Aligned_cols=24 Identities=21% Similarity=0.203 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 66 ESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 66 ~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
+.+...|+..|++.|...+....+
T Consensus 69 ~~d~~~Aid~a~~kl~rqL~k~k~ 92 (93)
T cd00552 69 AEDLYAAIDLAVDKLERQLRKYKE 92 (93)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhcc
Confidence 348999999999999998887654
No 58
>PF00668 Condensation: Condensation domain; InterPro: IPR001242 This domain is found in many multi-domain enzymes which synthesize peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non-ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (pp-binding). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site []. ; PDB: 2JGP_A 2VSQ_A 1L5A_A 2JUG_A 1Q9J_A.
Probab=34.67 E-value=49 Score=23.07 Aligned_cols=38 Identities=13% Similarity=0.196 Sum_probs=26.6
Q ss_pred CCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 52 PLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 52 Pl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
+...++.+.+..++..++ +.|++|++.+.+.-+.|+..
T Consensus 24 ~~~~~~~~~~~l~~~~d~-~~l~~A~~~~~~~h~~Lr~~ 61 (301)
T PF00668_consen 24 SSSYNIAFVFELDGPIDI-ERLRQALERLIARHPILRTR 61 (301)
T ss_dssp STTTEEEEEEEEEES--H-HHHHHHHHHHHHH-GGGGEE
T ss_pred CCcEEEEEEEEecCccch-HHHhhhhHhhhhhhhhhhhe
Confidence 334566777777777665 89999999999988777643
No 59
>PRK04207 glyceraldehyde-3-phosphate dehydrogenase; Provisional
Probab=34.56 E-value=2e+02 Score=22.38 Aligned_cols=51 Identities=20% Similarity=0.346 Sum_probs=37.7
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHH
Q psy11162 26 HTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITD 79 (91)
Q Consensus 26 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~ 79 (91)
|+ |..++..| -+-+|.....|+|-+.-+-.-+.+++++..+. +.+.+++++
T Consensus 193 ~~-g~~v~~vl-p~l~i~~~avrVPv~~gh~~~v~v~l~~~~t~-eev~~~l~~ 243 (341)
T PRK04207 193 HH-GPDVKTVL-PDLDITTMAVKVPTTLMHMHSVNVELKKPVTK-EEVLEALEN 243 (341)
T ss_pred Cc-hhHHHhhC-CCCceEEEEEEcCCCCceEEEEEEEECCCCCH-HHHHHHHHh
Confidence 44 66676666 33348888899999999999999999887665 555556654
No 60
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=32.28 E-value=1.5e+02 Score=22.50 Aligned_cols=47 Identities=15% Similarity=0.140 Sum_probs=33.5
Q ss_pred cCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q psy11162 38 KDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLF 87 (91)
Q Consensus 38 ~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l 87 (91)
..+++..--|-+-=|+ -.+++++..-....++|++|++.+.+.++.-
T Consensus 205 ~~~~~~v~i~~ig~P~---Y~i~~~~~d~k~~~~~l~~~~~~~~~~i~~~ 251 (262)
T PRK03987 205 KYEDVEVEIYYVGAPR---YRIDVTAPDYKTAEKALKKIAERAIKVIKKL 251 (262)
T ss_pred CCCCCcEEEEEECCCe---EEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566666666666665 5677777655567889999999988887653
No 61
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=31.09 E-value=90 Score=19.52 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 65 AESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 65 ~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.+.+|.++|...+..|.++++.+.-.
T Consensus 7 ~s~~p~~~Ls~vl~~LqDE~~hm~~e 32 (79)
T PF06657_consen 7 PSQSPGEALSEVLKALQDEFGHMKME 32 (79)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35589999999999999999887643
No 62
>PHA02243 hypothetical protein
Probab=30.97 E-value=68 Score=22.66 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=22.3
Q ss_pred CceeeeeecCCCCCceEEEEEecCCcc---hHHHHHH
Q psy11162 1 MIRKIIKELDTKVPNAAIFTVNKEDHT---LGNMIRN 34 (91)
Q Consensus 1 ~~~kv~~~~~~k~~n~~~~~i~~EdHT---lgNlLr~ 34 (91)
||+.+.+.-+.+ +++|.+||.| |||.|..
T Consensus 83 mi~ei~iyt~~~-----~iti~~e~ys~~~l~~~~~~ 114 (160)
T PHA02243 83 MIQEIDIYTQGK-----TITIDNEHYSSDDLGEVLNK 114 (160)
T ss_pred eeeEEEEEeccc-----EEEeccccccHHHHHHHHHH
Confidence 677777777666 7999999998 6777653
No 63
>PLN02231 alanine transaminase
Probab=30.48 E-value=2.2e+02 Score=23.52 Aligned_cols=57 Identities=12% Similarity=0.128 Sum_probs=38.5
Q ss_pred HHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162 32 IRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF 91 (91)
Q Consensus 32 Lr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~f 91 (91)
+...|++..+|.+.--+--.+..+.-.+|+.. . .+.+.+++|+++|.+.++.+-++|
T Consensus 476 ~~~~Ll~~~GV~vvPGs~Fg~~~g~~~~Rit~--~-~~~e~l~eal~RL~~~~~~~~~~~ 532 (534)
T PLN02231 476 YCKRLLNATGIVVVPGSGFGQVPGTWHFRCTI--L-PQEDKIPAIVSRLTEFHKSFMDEF 532 (534)
T ss_pred HHHHHHHhcCEEEeCCcccCCCCCCCeEEEEe--C-CCHHHHHHHHHHHHHHHHHHHHHh
Confidence 45567766677665333222333445577754 2 477999999999999999988876
No 64
>PHA02766 hypothetical protein; Provisional
Probab=30.35 E-value=46 Score=20.48 Aligned_cols=49 Identities=24% Similarity=0.320 Sum_probs=30.6
Q ss_pred ceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHH
Q psy11162 15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMN 75 (91)
Q Consensus 15 n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~ 75 (91)
-.+.|+|..||.-- |.+- .|+. --.||.++++++|.|+.-.+-.+|+.-
T Consensus 15 fkisfeineedyqq-------liel---afsq--fiyplndnieikintkeladnekally 63 (73)
T PHA02766 15 FKISFEINEEDYQQ-------LIEL---AFSQ--FIYPLNDNIEIKINTKELADNEKALLY 63 (73)
T ss_pred EEEEEEECHHHHHH-------HHHH---HHHh--heeeCCCceEEEechHhhccchhhHhH
Confidence 35678888888642 1111 1222 236899999999999865555555543
No 65
>PTZ00377 alanine aminotransferase; Provisional
Probab=30.12 E-value=2.2e+02 Score=22.69 Aligned_cols=57 Identities=11% Similarity=0.163 Sum_probs=37.5
Q ss_pred HHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162 32 IRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEERF 91 (91)
Q Consensus 32 Lr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~f 91 (91)
+...+++..+|.+..-..-.+....-.+|+-.. .+.+.+++|+++|.+.++.+.++|
T Consensus 424 ~~~~ll~~~gV~v~pG~~F~~~~~~~~~Rls~~---~~~e~l~~~l~rl~~~~~~~~~~~ 480 (481)
T PTZ00377 424 YCLELLESTGIVVVPGSGFGQKPGTYHFRITIL---PPEEQIEEMVKKIKEFHESFMKKY 480 (481)
T ss_pred HHHHHHHHcCEEEeCCcccCCCCCCCEEEEEEC---CCHHHHHHHHHHHHHHHHHHHHhh
Confidence 344666677777663332222222346777653 356899999999999999988876
No 66
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=29.28 E-value=1e+02 Score=23.14 Aligned_cols=36 Identities=6% Similarity=0.075 Sum_probs=23.5
Q ss_pred eeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 44 FAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 44 fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
.++|-+||++... .+.....+.+.+|++++-+.+..
T Consensus 5 v~~~~~~H~~~~~-------~~~~~~~~~~~~al~~~~~~l~~ 40 (268)
T cd07367 5 VGAAATSHILMSP-------KGVEDQAARVVQGMAEIGRRVRE 40 (268)
T ss_pred EEEEecCCcCcCC-------CCchHHHHHHHHHHHHHHHHHHH
Confidence 5789999976442 33334556677777777666643
No 67
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=29.27 E-value=1.5e+02 Score=18.43 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=24.7
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 58 ILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 58 ~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
.++++..+. +...|+..|++.|...+....+.
T Consensus 60 ~l~a~~~~~-d~y~Aid~a~~klerqL~k~k~k 91 (95)
T PRK10470 60 EIHASAEGQ-DMYAAIDGLIDKLARQLTKHKDK 91 (95)
T ss_pred EEEEEEecC-cHHHHHHHHHHHHHHHHHHHHHH
Confidence 456655544 89999999999999988776654
No 68
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=29.04 E-value=1.4e+02 Score=18.17 Aligned_cols=31 Identities=23% Similarity=0.233 Sum_probs=23.9
Q ss_pred EEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 59 LRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 59 l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
+++...+ .++..|+..|++.|...+....++
T Consensus 61 l~a~~~~-~d~~~Aid~a~~klerql~k~k~k 91 (95)
T TIGR00741 61 IRASAEH-EDMYAAIDLAIDKLERQLRKLKEK 91 (95)
T ss_pred EEEEEec-CcHHHHHHHHHHHHHHHHHHHHhh
Confidence 5555443 489999999999999988876653
No 69
>KOG1521|consensus
Probab=27.98 E-value=1.5e+02 Score=23.78 Aligned_cols=44 Identities=18% Similarity=0.295 Sum_probs=34.0
Q ss_pred eeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 42 VLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 42 V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
+.+-|-.-.| ..+.|.+.|...|...+.+|+.-|...|..+++.
T Consensus 293 ~V~LgrvrdH-----fIFsvestgal~p~~lf~eavkvle~Kc~al~~~ 336 (338)
T KOG1521|consen 293 KVQLGRVRDH-----FIFSVESTGALKPEVLFEEAVKVLEEKCRALRDE 336 (338)
T ss_pred heeeccccce-----EEEEeecccCCCchhhHHHHHHHHHHHHHHHhhc
Confidence 3445554445 6688888888899999999999999999888764
No 70
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=27.80 E-value=43 Score=23.40 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=21.7
Q ss_pred HHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEe
Q psy11162 30 NMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63 (91)
Q Consensus 30 NlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt 63 (91)
-.+=.++.++|+|+|||-.-.- ..+|++-
T Consensus 47 K~~yKqik~np~vefcg~~kdg-----~~vrlrg 75 (132)
T COG5015 47 KPYYKQIKKNPEVEFCGMDKDG-----VMVRLRG 75 (132)
T ss_pred hHHHHHHhhCCCeEEEEecCCc-----eEEEEee
Confidence 3566889999999999987654 4566553
No 71
>KOG1521|consensus
Probab=27.62 E-value=65 Score=25.72 Aligned_cols=36 Identities=14% Similarity=0.200 Sum_probs=29.3
Q ss_pred eeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC
Q psy11162 4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD 39 (91)
Q Consensus 4 kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~ 39 (91)
.+.+...+...+.++|-+.|-|-.++|++|-.|+..
T Consensus 45 ~~~V~iv~~~~~~leFDligIda~IANAfRRILiaE 80 (338)
T KOG1521|consen 45 NFKVDIVSLDEETLEFDLIGIDASIANAFRRILIAE 80 (338)
T ss_pred ceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHhh
Confidence 344455566668999999999999999999999864
No 72
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=27.58 E-value=2.8e+02 Score=21.17 Aligned_cols=59 Identities=17% Similarity=0.190 Sum_probs=36.9
Q ss_pred chHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy11162 27 TLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE 88 (91)
Q Consensus 27 TlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~ 88 (91)
.|.-.|+......|+|.++.|--....... .+.|+... .-.++++.+++.+........
T Consensus 192 ~la~~L~~i~~~~~~~~i~s~p~~~~~~~~-~~~i~~~~--~~~~~~~~~~~~~~~~i~~~~ 250 (255)
T COG1058 192 SLAPTLKDLQDEQPNVTIASYPKDGEVRLR-ELVIRAEA--RDEEEADALLRWLEGRLRARG 250 (255)
T ss_pred HHHHHHHHHHhcCCCCEEEecCCCCceecc-ceEEEEec--CCHHHHHHHHHHHHHHHHHhh
Confidence 477788888888899988877544433221 44466543 345666777776666655443
No 73
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=27.48 E-value=1e+02 Score=18.69 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=16.1
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHH
Q psy11162 58 ILRIQTTAESTPHDALMNAITDL 80 (91)
Q Consensus 58 ~l~Iqt~~~~~p~~al~~a~~~l 80 (91)
..+|++..+..-.++|++||+..
T Consensus 8 r~~vkvtp~~~l~~VL~eac~k~ 30 (65)
T PF11470_consen 8 RFKVKVTPNTTLNQVLEEACKKF 30 (65)
T ss_dssp EEEE---TTSBHHHHHHHHHHHT
T ss_pred EEEEEECCCCCHHHHHHHHHHHc
Confidence 46777777778899999999764
No 74
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=26.85 E-value=1.9e+02 Score=19.07 Aligned_cols=44 Identities=18% Similarity=0.322 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHH
Q psy11162 29 GNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL 80 (91)
Q Consensus 29 gNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l 80 (91)
.+.++..|+..|+++..+=.-+ +++.+.|++++. +-+-+.++.+
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~----GKlVVVie~~~~----~~l~~tie~i 63 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE----GKLVVVIEAEDS----ETLLETIESI 63 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC----ceEEEEEEcCch----HHHHHHHHHH
Confidence 4788999999999997764432 799999998754 4444444444
No 75
>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]. These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....
Probab=26.45 E-value=1.5e+02 Score=21.54 Aligned_cols=34 Identities=21% Similarity=0.523 Sum_probs=26.7
Q ss_pred CCceEEEEEecCCcchHHHHHHHHhcCCCeeeee
Q psy11162 13 VPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAG 46 (91)
Q Consensus 13 ~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAg 46 (91)
.+|...+.-....+++..+|+..|..+|++.+.|
T Consensus 171 ~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiig 204 (270)
T PF00437_consen 171 GPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIG 204 (270)
T ss_dssp CSSEEEEEEETTTBSHHHHHHHHTTS--SEEEES
T ss_pred ccceEEEEeecCcccHHHHHHHHhcCCCCccccc
Confidence 3566666666789999999999999999999877
No 76
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=25.34 E-value=1.2e+02 Score=25.30 Aligned_cols=33 Identities=27% Similarity=0.522 Sum_probs=25.4
Q ss_pred CceEEEEEecC-CcchHHHHHHHHhcCCCeeeee
Q psy11162 14 PNAAIFTVNKE-DHTLGNMIRNQLLKDPHVLFAG 46 (91)
Q Consensus 14 ~n~~~~~i~~E-dHTlgNlLr~~L~~~~~V~fAg 46 (91)
++...+++..+ +.|+.++|+..|.+||+|.+.|
T Consensus 359 ~~~~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vG 392 (564)
T TIGR02538 359 PGINQVNVNPKIGLTFAAALRSFLRQDPDIIMVG 392 (564)
T ss_pred CCceEEEeccccCCCHHHHHHHHhccCCCEEEeC
Confidence 34444555433 4799999999999999999988
No 77
>COG2033 Desulfoferrodoxin [Energy production and conversion]
Probab=25.11 E-value=52 Score=22.85 Aligned_cols=11 Identities=36% Similarity=0.909 Sum_probs=9.0
Q ss_pred eeeeCCCCCCCe
Q psy11162 45 AGYKQPHPLEHK 56 (91)
Q Consensus 45 AgY~vpHPl~~~ 56 (91)
.| .||||++++
T Consensus 57 VG-~IpHPmt~e 67 (126)
T COG2033 57 VG-EIPHPMTPE 67 (126)
T ss_pred Ec-ccCCCCCCc
Confidence 45 899999876
No 78
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=24.84 E-value=1.5e+02 Score=17.18 Aligned_cols=47 Identities=19% Similarity=0.198 Sum_probs=26.3
Q ss_pred CCCeeeeeeeCCCCCCCeeEEEEEeCCCC-CHHHHHHHHHHHHHHHHH
Q psy11162 39 DPHVLFAGYKQPHPLEHKFILRIQTTAES-TPHDALMNAITDLLAELS 85 (91)
Q Consensus 39 ~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~-~p~~al~~a~~~l~~~~~ 85 (91)
.-++.+..+..++...+.+.+++...... -..+.|+++++.+...++
T Consensus 27 I~~~~~~~~~~~~~~~~~~~~~~~v~~p~~~~~~~l~~~l~~l~~~~~ 74 (81)
T cd04869 27 IEDLSTETYSAPMSGTPLFKAQATLALPAGTDLDALREELEELCDDLN 74 (81)
T ss_pred eEEeEeeeecCCCCCcceEEEEEEEecCCCCCHHHHHHHHHHHHHHhc
Confidence 34444444444433445565565554321 246888888888776653
No 79
>COG4115 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.43 E-value=64 Score=20.94 Aligned_cols=24 Identities=33% Similarity=0.739 Sum_probs=19.6
Q ss_pred HHHHHHHhcCCCeeeeeeeCCCCCCCe
Q psy11162 30 NMIRNQLLKDPHVLFAGYKQPHPLEHK 56 (91)
Q Consensus 30 NlLr~~L~~~~~V~fAgY~vpHPl~~~ 56 (91)
|-|-..+.+|| |.|+--|-||...
T Consensus 28 ~~Li~~i~rdP---fkg~gkpEpLk~~ 51 (84)
T COG4115 28 NELIKEIKRDP---FKGIGKPEPLKGD 51 (84)
T ss_pred HHHHHHhccCc---cccCCCCccCccc
Confidence 55667788887 8999999999764
No 80
>cd07369 PydA_Rs_like PydA is a Class III Extradiol ring-cleavage dioxygenase required for the degradation of 3-hydroxy-4-pyridone (HP). This subfamily is composed of Rhizobium sp. PydA and similar proteins. PydA is required for the degradation of 3-hydroxy-4-pyridone (HP), an intermediate in the Leucaena toxin mimosine degradation pathway. It is a member of the class III extradiol dioxygenase family, a group of enzymes that use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=23.65 E-value=1.1e+02 Score=24.07 Aligned_cols=39 Identities=15% Similarity=-0.045 Sum_probs=24.2
Q ss_pred eeeeeCCC-CCC-CeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Q psy11162 44 FAGYKQPH-PLE-HKFILRIQTTAESTPHDALMNAITDLLAELSLF 87 (91)
Q Consensus 44 fAgY~vpH-Pl~-~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l 87 (91)
.+||.+|| |+. ..+.. +...-.+...+|++.+-+.+.++
T Consensus 5 v~a~~~sH~P~i~~~p~~-----~~~~~~~~~~~a~~~l~~~v~~~ 45 (329)
T cd07369 5 VAAIGMSHAPGALGWPDA-----PSPDVRARTEEATLKLGRTLTAA 45 (329)
T ss_pred heeeecCCCccccCCCCC-----CchHHHHHHHHHHHHHHHHHHHh
Confidence 36799999 554 33333 22234567777777777777654
No 81
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=23.65 E-value=1.4e+02 Score=22.66 Aligned_cols=24 Identities=17% Similarity=0.112 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 66 ESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 66 ~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
+++|..||.++.......|..++.
T Consensus 200 giDpE~ALr~a~~KF~~Rf~~~E~ 223 (248)
T TIGR00444 200 KTDAEIALQKANEKFERRFREVER 223 (248)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999998875
No 82
>PF11873 DUF3393: Domain of unknown function (DUF3393); InterPro: IPR024570 Membrane-bound lytic murein transglycosylase C (also known as murein hydrolase C), is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. This entry represents the N-terminal domain, whose function is currently not known.
Probab=23.62 E-value=1.1e+02 Score=22.62 Aligned_cols=26 Identities=27% Similarity=0.330 Sum_probs=20.9
Q ss_pred CCeeEEEEEeCCCCCHHHHHHHHHHH
Q psy11162 54 EHKFILRIQTTAESTPHDALMNAITD 79 (91)
Q Consensus 54 ~~~~~l~Iqt~~~~~p~~al~~a~~~ 79 (91)
.+.=.|+|.|-.+.+|.+.|++|+-.
T Consensus 94 Fd~G~I~VETi~~~~p~~~Lk~AIv~ 119 (204)
T PF11873_consen 94 FDKGTITVETIAQTDPKAHLKQAIVT 119 (204)
T ss_pred eeCCeEEEEecCCcCHHHHHHHHHHH
Confidence 34556889998888999999999854
No 83
>PRK13358 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=23.35 E-value=1e+02 Score=22.92 Aligned_cols=36 Identities=8% Similarity=0.157 Sum_probs=21.9
Q ss_pred eeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy11162 44 FAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSL 86 (91)
Q Consensus 44 fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~ 86 (91)
..+|-+|||+.... +..+-...+.++++++.+.+..
T Consensus 5 ~~~~~~pH~~~~~~-------~~~~~~~~~~~~l~~~~~~l~~ 40 (269)
T PRK13358 5 VGAFATSHVLMSSK-------GGEEQAKRVVEGMREIGRRLRE 40 (269)
T ss_pred heehcccccccCCC-------CchHHHHHHHHHHHHHHHHHHH
Confidence 46799999665433 1113345667777777766643
No 84
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.18 E-value=1.4e+02 Score=19.04 Aligned_cols=27 Identities=15% Similarity=0.233 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhC
Q psy11162 65 AESTPHDALMNAITDLLAELSLFEERF 91 (91)
Q Consensus 65 ~~~~p~~al~~a~~~l~~~~~~l~~~f 91 (91)
++..|.+++..++..+.+++..|+++|
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~l~~~~ 99 (99)
T cd04765 73 AAAIREEEAEERLPSIRAELLDLRDQL 99 (99)
T ss_pred ccccchhhHHHHHHHHHHHHHHHHhcC
Confidence 344788999999999999999998875
No 85
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=22.71 E-value=1.5e+02 Score=18.21 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=15.8
Q ss_pred EEEeCCCCCHHHHHHHHHHH
Q psy11162 60 RIQTTAESTPHDALMNAITD 79 (91)
Q Consensus 60 ~Iqt~~~~~p~~al~~a~~~ 79 (91)
.|++..|.+..++|.+||+.
T Consensus 13 ~V~vrpg~ti~d~L~~~c~k 32 (72)
T cd01760 13 VVPVRPGMSVRDVLAKACKK 32 (72)
T ss_pred EEEECCCCCHHHHHHHHHHH
Confidence 45556778999999999974
No 86
>TIGR00978 asd_EA aspartate-semialdehyde dehydrogenase (non-peptidoglycan organisms). Two closely related families of aspartate-semialdehyde dehydrogenase are found. They differ by a deep split in phylogenetic and percent identity trees and in gap patterns. Separate models are built for the two types in order to exclude the USG-1 protein, found in several species, which is specifically related to the Bacillus subtilis type of aspartate-semialdehyde dehydrogenase. Members of this type are found primarily in organisms that lack peptidoglycan.
Probab=22.09 E-value=3.1e+02 Score=21.08 Aligned_cols=56 Identities=14% Similarity=0.090 Sum_probs=40.3
Q ss_pred cCCcchHHHHHHHHhc---------CCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHH
Q psy11162 23 KEDHTLGNMIRNQLLK---------DPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITD 79 (91)
Q Consensus 23 ~EdHTlgNlLr~~L~~---------~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~ 79 (91)
+++|-...=+++.|-+ .-.|.|..+++|-.--.-..+.++++...++ +.+.+++++
T Consensus 198 ~~ehrh~~Ei~~il~~~~~~~~~~~~~~v~~t~~~vPv~rG~~~tv~v~l~~~~~~-~~i~~~~~~ 262 (341)
T TIGR00978 198 GEEEKIERETRKILGKLENGKIEPAPFSVSATTTRVPVLDGHTESVHVEFDKKFDI-EEIREALKS 262 (341)
T ss_pred HHHHHHHHHHHHHhCccccCcccCCCceEEEEEEEcCccccEEEEEEEEeCCCCCH-HHHHHHHHh
Confidence 4557666667777754 3359999999999988888899988876655 445555543
No 87
>PF01933 UPF0052: Uncharacterised protein family UPF0052; InterPro: IPR002882 This entry contains LPPG:Fo 2-phospho-L-lactate transferase (CofD) and related sequences of unknown function belong to unidentified protein family UPF0052. CofD catalyses the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) [] but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. ; PDB: 2HZB_A 2O2Z_C 3CGW_A 3C3E_D 3C3D_D 2PPV_A 2P0Y_A 2Q7X_B.
Probab=21.98 E-value=59 Score=25.15 Aligned_cols=15 Identities=40% Similarity=0.662 Sum_probs=10.9
Q ss_pred cCCcchHHHHHHHHh
Q psy11162 23 KEDHTLGNMIRNQLL 37 (91)
Q Consensus 23 ~EdHTlgNlLr~~L~ 37 (91)
-.+|++||+++..+.
T Consensus 84 l~~hslGNl~l~~~~ 98 (300)
T PF01933_consen 84 LAGHSLGNLFLTALL 98 (300)
T ss_dssp GTT-BHHHHHHHHHH
T ss_pred HhhCchhHHHHHHHH
Confidence 468999999996653
No 88
>PRK01215 competence damage-inducible protein A; Provisional
Probab=21.81 E-value=3e+02 Score=20.71 Aligned_cols=67 Identities=13% Similarity=0.174 Sum_probs=36.4
Q ss_pred EEEEecCC-cchHHHHHHHHhcCCCeee--e--eeeCCCCCCCeeEEEEEeCCC--CCHHHHHHHHHHHHHHHHHHH
Q psy11162 18 IFTVNKED-HTLGNMIRNQLLKDPHVLF--A--GYKQPHPLEHKFILRIQTTAE--STPHDALMNAITDLLAELSLF 87 (91)
Q Consensus 18 ~~~i~~Ed-HTlgNlLr~~L~~~~~V~f--A--gY~vpHPl~~~~~l~Iqt~~~--~~p~~al~~a~~~l~~~~~~l 87 (91)
++.+.|-+ =+|.-.|.....+.|+|.+ + ||. +|+ ..+.+|+...+. ....+++..+.+.|.+.+..+
T Consensus 183 ~~~~~Gi~Es~l~~~l~~l~~~~~~~~~~s~p~~~~-~~~--~~v~vrl~~~~~~~~~~~~~~~~~~~~i~~~~~~~ 256 (264)
T PRK01215 183 SILVEGVMESDLAPYVKELVKKYDRVYVKSHPKGYE-VSK--PILEIQIAGSGEREEEAKVKVEKVLEELKELIKKL 256 (264)
T ss_pred EEEECCCCHHHHHHHHHHHHHhCCCCEEecCcccee-cCC--CeEEEEEEEecCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 44554422 3566677777677789987 4 244 343 567788876543 112223344555555554443
No 89
>PRK09389 (R)-citramalate synthase; Provisional
Probab=21.81 E-value=4.6e+02 Score=21.59 Aligned_cols=60 Identities=18% Similarity=0.226 Sum_probs=41.1
Q ss_pred EecCCcchHHHHHHHHhcC--CCeeeeeeeCC--CCCCCeeEEEEEeCC--------CCCHHHHHHHHHHHHHH
Q psy11162 21 VNKEDHTLGNMIRNQLLKD--PHVLFAGYKQP--HPLEHKFILRIQTTA--------ESTPHDALMNAITDLLA 82 (91)
Q Consensus 21 i~~EdHTlgNlLr~~L~~~--~~V~fAgY~vp--HPl~~~~~l~Iqt~~--------~~~p~~al~~a~~~l~~ 82 (91)
+..+| |-.+++..+... +...+-+|++- ........++++.+| |--|++|+-+|++++..
T Consensus 356 ~~~~e--l~~l~~~~~~~~~~~~~~l~~~~v~~~~~~~~~a~v~~~~~g~~~~~~~~G~GpvdA~~~Al~~~~~ 427 (488)
T PRK09389 356 VTDAD--LLAIAEDVLGIERERKVKLDELTVVSGNKVTPTASVKLNVDGEEIVEAGTGVGPVDAAINAVRKALS 427 (488)
T ss_pred cCHHH--HHHHHHHHhhhcCCCCEEEEEEEEEECCCCCcEEEEEEEECCEEEEEEEEecCHHHHHHHHHHHHhC
Confidence 44444 888888877654 57888888873 223455666665544 23599999999998764
No 90
>PF04263 TPK_catalytic: Thiamin pyrophosphokinase, catalytic domain; InterPro: IPR007371 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0005524 ATP binding, 0009229 thiamine diphosphate biosynthetic process; PDB: 2F17_B 1IG3_B 3S4Y_B 2OMK_B 1IG0_A 3MEL_B 3CQ9_A 3LM8_B 3K94_B 3L8M_B ....
Probab=21.80 E-value=24 Score=23.69 Aligned_cols=14 Identities=36% Similarity=0.206 Sum_probs=9.9
Q ss_pred CCcchHHHHHHHHh
Q psy11162 24 EDHTLGNMIRNQLL 37 (91)
Q Consensus 24 EdHTlgNlLr~~L~ 37 (91)
-||||+|+-.-.=.
T Consensus 98 ~DH~lanl~~l~~~ 111 (123)
T PF04263_consen 98 FDHTLANLNLLYKY 111 (123)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 59999998654433
No 91
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=21.10 E-value=2.3e+02 Score=17.79 Aligned_cols=68 Identities=12% Similarity=0.152 Sum_probs=39.7
Q ss_pred eeecCCCCCceEEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCCeeEEEEEeCCCCCHHHHHHHHHHHHH
Q psy11162 6 IKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDLL 81 (91)
Q Consensus 6 ~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~l~Iqt~~~~~p~~al~~a~~~l~ 81 (91)
++..+...-...++++...+..-+..|...|...++|+=.-|.-. .+.|.=+.+.+- +.|+..+...+
T Consensus 13 KF~~~~~~~~~~s~~f~~~~~a~~spLA~~Lf~i~gV~~Vf~~~d-------fItVtK~~~~~W-~~l~~~I~~~I 80 (87)
T PF08712_consen 13 KFVLDEPLLPGGSFEFKSAEEASDSPLAQALFAIPGVKSVFIGDD-------FITVTKNPDADW-EDLKPEIREVI 80 (87)
T ss_dssp EEEESS-SSTS---EEESSS-TTS-HHHHHHHTSTTEEEEEEETT-------EEEEEE-TTS-H-HHHHHHHHHHT
T ss_pred EEECCceeecCccEEeCChHHcccCHHHHHhcCCCCEeEEEEECC-------EEEEeeCCCCCH-HHHHHHHHHHH
Confidence 344456566666888888888888999999999999986555444 366654444444 44544444443
No 92
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=21.02 E-value=1.6e+02 Score=22.76 Aligned_cols=26 Identities=35% Similarity=0.372 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy11162 64 TAESTPHDALMNAITDLLAELSLFEE 89 (91)
Q Consensus 64 ~~~~~p~~al~~a~~~l~~~~~~l~~ 89 (91)
.|+.+|.+|++++.+++...++..++
T Consensus 410 ~g~~t~~eal~~a~~~~~~~l~~~~~ 435 (438)
T PRK10974 410 TGKKTPQQALDSAVERGNQLLRRFEK 435 (438)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 34568999999999999888887765
No 93
>PF04455 Saccharop_dh_N: LOR/SDH bifunctional enzyme conserved region ; InterPro: IPR007545 Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to saccharopine dehydrogenase conserved region (IPR005097 from INTERPRO) in eukaryotes [, ].; PDB: 3C2Q_B 3MGJ_A.
Probab=20.95 E-value=1.8e+02 Score=19.23 Aligned_cols=38 Identities=16% Similarity=0.022 Sum_probs=28.6
Q ss_pred ceeeeeecCCCCCceEEEEEecCCcchHHHHHHHHhcC
Q psy11162 2 IRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKD 39 (91)
Q Consensus 2 ~~kv~~~~~~k~~n~~~~~i~~EdHTlgNlLr~~L~~~ 39 (91)
|.++.+-.....++.+.+++.++|+...+-+-++|.+.
T Consensus 34 i~~~~vG~~~~d~S~a~l~V~a~d~~~L~~Il~~L~~l 71 (103)
T PF04455_consen 34 ILEFDVGKSKDDTSYARLQVSAPDEEHLDEILDELHQL 71 (103)
T ss_dssp EEEEE--SSTTS-EEEEEEEEESSHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCCCCceeEEEEEecCCHHHHHHHHHHHHHH
Confidence 44566666777889999999999999888888888764
No 94
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=20.94 E-value=1.4e+02 Score=18.04 Aligned_cols=21 Identities=29% Similarity=0.213 Sum_probs=15.5
Q ss_pred EEEEeCCCCCHHHHHHHHHHH
Q psy11162 59 LRIQTTAESTPHDALMNAITD 79 (91)
Q Consensus 59 l~Iqt~~~~~p~~al~~a~~~ 79 (91)
-.|+...|.+..++|.+||+.
T Consensus 13 t~V~vrpg~ti~d~L~~~~~k 33 (71)
T PF02196_consen 13 TVVQVRPGMTIRDALSKACKK 33 (71)
T ss_dssp EEEEE-TTSBHHHHHHHHHHT
T ss_pred EEEEEcCCCCHHHHHHHHHHH
Confidence 445566778999999999864
No 95
>cd07930 bacterial_phosphagen_kinase Phosphagen (guanidino) kinases found in bacteria. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, such as phosphocreatine (PCr) or phosphoarginine, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. This subfamily is specific to bacteria and lacks an N-terminal domain, which otherwise forms part of the substrate binding site. Most of the catalytic residues are found in the larger C-terminal domain, however, which appears conserved in these bacterial proteins. Their functions have not been characterized.
Probab=20.72 E-value=2.6e+02 Score=20.76 Aligned_cols=20 Identities=30% Similarity=0.189 Sum_probs=13.3
Q ss_pred EEEEe-CCCCCHHHHHHHHHH
Q psy11162 59 LRIQT-TAESTPHDALMNAIT 78 (91)
Q Consensus 59 l~Iqt-~~~~~p~~al~~a~~ 78 (91)
||||+ ..|.++.+|.++|.+
T Consensus 102 lrI~~~~~G~~l~~~~~r~~~ 122 (232)
T cd07930 102 LRIQCLLPGLQLEEAYERADK 122 (232)
T ss_pred EEEEEEeCCCCHHHHHHHHHH
Confidence 67776 344588777777653
No 96
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.49 E-value=1.5e+02 Score=22.44 Aligned_cols=35 Identities=14% Similarity=0.221 Sum_probs=28.6
Q ss_pred eeeecCCCCCceEEEEEecCCcchH-HHHHHHHhcC
Q psy11162 5 IIKELDTKVPNAAIFTVNKEDHTLG-NMIRNQLLKD 39 (91)
Q Consensus 5 v~~~~~~k~~n~~~~~i~~EdHTlg-NlLr~~L~~~ 39 (91)
|+|..+-..++-..+++.|||-++. |+|+++--+-
T Consensus 31 V~~~i~~~~~~wv~vtl~GeD~eva~Nll~eefGei 66 (225)
T PF09883_consen 31 VEWDIGITKDDWVKVTLEGEDEEVAANLLREEFGEI 66 (225)
T ss_pred EEEEeccccCCceEEEEecCcHHHHHHHHHHHhCCC
Confidence 4566666677889999999999985 9999987765
No 97
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=20.40 E-value=2.9e+02 Score=18.77 Aligned_cols=44 Identities=23% Similarity=0.248 Sum_probs=25.6
Q ss_pred CCCeeeeeeeCCCCCCCeeEE----EEEeCCCCCHHHHHHHHHHHHHH
Q psy11162 39 DPHVLFAGYKQPHPLEHKFIL----RIQTTAESTPHDALMNAITDLLA 82 (91)
Q Consensus 39 ~~~V~fAgY~vpHPl~~~~~l----~Iqt~~~~~p~~al~~a~~~l~~ 82 (91)
||+..-.||-+--...+.+.+ .|+|+++.+..+-+..-.+.|.+
T Consensus 6 DPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~ 53 (154)
T cd00529 6 DPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNE 53 (154)
T ss_pred ccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHH
Confidence 788888999886443455555 67877443443333333333333
No 98
>PRK09294 acyltransferase PapA5; Provisional
Probab=20.37 E-value=1.9e+02 Score=22.30 Aligned_cols=35 Identities=17% Similarity=0.070 Sum_probs=27.3
Q ss_pred CeeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q psy11162 55 HKFILRIQTTAESTPHDALMNAITDLLAELSLFEER 90 (91)
Q Consensus 55 ~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~~l~~~ 90 (91)
..+.+.+..+|..++ ++|++|++.+......|+..
T Consensus 22 ~~~~~~~~l~g~lD~-~~L~~Al~~l~~rhp~Lr~~ 56 (416)
T PRK09294 22 AFTGYTAHLRGVLDI-DALSDAFDALLRAHPVLAAH 56 (416)
T ss_pred ceEEEEEEEcCCCCH-HHHHHHHHHHHHhCHHhhEE
Confidence 334467777788888 99999999999988877643
No 99
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=20.24 E-value=1.9e+02 Score=16.68 Aligned_cols=67 Identities=7% Similarity=0.110 Sum_probs=38.2
Q ss_pred EEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCC-CCeeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy11162 17 AIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPL-EHKFILRIQTTAESTPHDALMNAITDLLAELS 85 (91)
Q Consensus 17 ~~~~i~~EdHTlgNlLr~~L~~~~~V~fAgY~vpHPl-~~~~~l~Iqt~~~~~p~~al~~a~~~l~~~~~ 85 (91)
+.|++.++-=+|.++|...-...=++.-- .+.|-+- ..+..+.|...+.. -...++++++.|.+.+.
T Consensus 2 l~~~l~d~pG~L~~vL~~f~~~~vni~~I-~Srp~~~~~~~~~f~id~~~~~-~~~~~~~~l~~l~~~~~ 69 (75)
T cd04880 2 LVFSLKNKPGALAKALKVFAERGINLTKI-ESRPSRKGLWEYEFFVDFEGHI-DDPDVKEALEELKRVTE 69 (75)
T ss_pred EEEEeCCcCCHHHHHHHHHHHCCCCEEEE-EeeecCCCCceEEEEEEEECCC-CCHHHHHHHHHHHHhCC
Confidence 45666665566777776665555555444 4445443 45566667666531 12566666666666554
Done!