Query 033831
Match_columns 110
No_of_seqs 104 out of 470
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 06:47:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033831.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033831hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4392 RNA polymerase, subuni 100.0 4.9E-45 1.1E-49 254.0 12.1 109 1-109 1-109 (117)
2 cd06926 RNAP_II_RPB11 RPB11 su 100.0 1.5E-39 3.3E-44 220.6 12.1 93 13-105 1-93 (93)
3 PF13656 RNA_pol_L_2: RNA poly 100.0 6.8E-37 1.5E-41 201.2 9.1 77 29-105 1-77 (77)
4 cd07029 RNAP_I_III_AC19 AC19 s 100.0 1.6E-36 3.5E-41 202.9 10.6 82 24-105 4-85 (85)
5 PRK01146 DNA-directed RNA poly 100.0 7.1E-36 1.5E-40 199.8 10.6 83 21-103 3-85 (85)
6 cd06927 RNAP_L L subunit of Ar 100.0 2.6E-35 5.7E-40 196.3 10.2 78 25-102 5-82 (83)
7 cd07027 RNAP_RPB11_like RPB11 100.0 5.1E-35 1.1E-39 194.9 10.4 78 25-102 5-82 (83)
8 COG1761 RPB11 DNA-directed RNA 100.0 3.6E-33 7.8E-38 191.5 12.2 90 16-105 2-91 (99)
9 KOG3438 DNA-directed RNA polym 100.0 2.3E-32 5E-37 187.6 9.5 83 26-108 13-95 (105)
10 cd00460 RNAP_RPB11_RPB3 RPB11 99.9 1.4E-26 3E-31 154.4 9.8 76 25-101 5-86 (86)
11 PF01193 RNA_pol_L: RNA polyme 99.7 1.1E-17 2.3E-22 106.2 5.1 65 31-99 1-66 (66)
12 PRK14979 DNA-directed RNA poly 95.9 0.043 9.2E-07 41.8 7.0 51 53-107 138-188 (195)
13 cd06928 RNAP_alpha_NTD N-termi 95.7 0.025 5.4E-07 43.3 5.0 46 55-100 163-214 (215)
14 cd07028 RNAP_RPB3_like RPB3 su 95.5 0.046 9.9E-07 41.9 6.2 52 51-103 160-211 (212)
15 TIGR02027 rpoA DNA-directed RN 95.2 0.064 1.4E-06 43.0 6.3 49 55-103 154-208 (297)
16 smart00662 RPOLD RNA polymeras 95.2 0.045 9.8E-07 41.9 5.2 45 56-100 163-223 (224)
17 PRK00783 DNA-directed RNA poly 94.8 0.029 6.3E-07 43.6 3.1 36 18-55 2-38 (263)
18 CHL00013 rpoA RNA polymerase a 94.6 0.094 2E-06 42.7 5.8 49 55-103 170-223 (327)
19 PRK05182 DNA-directed RNA poly 94.6 0.11 2.3E-06 42.0 6.0 48 56-103 172-225 (310)
20 CHL00013 rpoA RNA polymerase a 94.2 0.096 2.1E-06 42.7 5.1 47 19-65 10-61 (327)
21 PRK05182 DNA-directed RNA poly 93.8 0.15 3.3E-06 41.1 5.4 47 18-64 8-59 (310)
22 cd07028 RNAP_RPB3_like RPB3 su 93.8 0.07 1.5E-06 40.9 3.4 33 25-57 7-40 (212)
23 cd07030 RNAP_D D subunit of Ar 93.7 0.067 1.4E-06 41.5 3.2 36 18-55 2-38 (259)
24 cd07031 RNAP_II_RPB3 RPB3 subu 93.5 0.17 3.6E-06 39.9 5.1 40 68-107 225-264 (265)
25 cd06928 RNAP_alpha_NTD N-termi 93.4 0.13 2.8E-06 39.3 4.2 40 25-64 5-49 (215)
26 PRK14979 DNA-directed RNA poly 92.7 0.23 5E-06 37.8 4.7 40 20-60 5-45 (195)
27 COG0202 RpoA DNA-directed RNA 92.0 0.35 7.5E-06 39.3 5.1 45 19-63 7-54 (317)
28 cd07031 RNAP_II_RPB3 RPB3 subu 92.0 0.4 8.7E-06 37.8 5.4 41 18-60 2-43 (265)
29 smart00662 RPOLD RNA polymeras 91.0 0.33 7.3E-06 37.1 3.9 33 31-63 2-35 (224)
30 PRK00783 DNA-directed RNA poly 89.1 1.2 2.5E-05 34.6 5.6 41 67-107 221-261 (263)
31 cd07030 RNAP_D D subunit of Ar 86.6 2 4.3E-05 33.3 5.5 37 68-104 222-258 (259)
32 TIGR02027 rpoA DNA-directed RN 85.4 1.1 2.3E-05 36.0 3.6 29 36-64 11-40 (297)
33 cd07032 RNAP_I_II_AC40 AC40 su 85.0 2.4 5.3E-05 34.1 5.4 37 67-103 254-290 (291)
34 PRK02261 methylaspartate mutas 70.8 5.2 0.00011 28.4 3.0 37 28-64 4-42 (137)
35 COG2805 PilT Tfp pilus assembl 69.8 2.9 6.4E-05 34.6 1.7 26 35-60 180-205 (353)
36 cd02070 corrinoid_protein_B12- 66.0 13 0.00029 27.5 4.5 38 29-66 84-123 (201)
37 cd02071 MM_CoA_mut_B12_BD meth 65.6 19 0.00042 24.5 5.0 25 31-55 3-27 (122)
38 cd02067 B12-binding B12 bindin 65.2 18 0.0004 24.0 4.7 34 31-64 3-38 (119)
39 cd04905 ACT_CM-PDT C-terminal 60.5 38 0.00083 21.0 6.6 68 30-99 3-71 (80)
40 TIGR02370 pyl_corrinoid methyl 59.6 11 0.00025 27.9 3.1 39 28-66 85-125 (197)
41 COG0202 RpoA DNA-directed RNA 58.0 20 0.00044 29.1 4.5 40 68-107 187-226 (317)
42 cd02069 methionine_synthase_B1 57.5 12 0.00027 28.3 3.1 39 28-66 89-129 (213)
43 KOG2972 Uncharacterized conser 46.3 59 0.0013 26.2 5.3 53 40-92 92-145 (276)
44 KOG1522 RNA polymerase II, sub 43.8 57 0.0012 26.3 4.9 64 44-107 187-267 (285)
45 PF04912 Dynamitin: Dynamitin 41.1 31 0.00067 28.3 3.1 98 1-108 4-113 (388)
46 PRK00549 competence damage-ind 41.0 1.3E+02 0.0028 25.1 6.9 54 40-99 191-244 (414)
47 PF06657 Cep57_MT_bd: Centroso 40.3 79 0.0017 20.5 4.4 29 79-107 7-35 (79)
48 PLN02231 alanine transaminase 37.7 1.5E+02 0.0033 25.4 7.0 58 46-106 476-533 (534)
49 cd07032 RNAP_I_II_AC40 AC40 su 36.8 45 0.00097 26.9 3.4 34 18-53 2-35 (291)
50 COG2804 PulE Type II secretory 34.9 34 0.00074 29.8 2.5 25 36-60 310-334 (500)
51 PRK01215 competence damage-ind 34.6 2.3E+02 0.0049 22.2 7.4 45 32-79 183-232 (264)
52 PF11470 TUG-UBL1: GLUT4 regul 34.5 61 0.0013 20.4 3.1 24 71-94 7-30 (65)
53 PRK12729 fliE flagellar hook-b 34.4 1.2E+02 0.0027 21.7 5.0 15 82-96 57-71 (127)
54 PF03633 Glyco_hydro_65C: Glyc 34.2 31 0.00067 20.2 1.6 24 18-42 29-52 (54)
55 PF02482 Ribosomal_S30AE: Sigm 34.0 97 0.0021 19.6 4.1 33 72-105 62-94 (97)
56 COG1544 Ribosome-associated pr 32.6 1.7E+02 0.0037 20.2 6.1 27 81-107 70-96 (110)
57 PTZ00377 alanine aminotransfer 31.5 2.2E+02 0.0048 23.6 6.8 58 46-106 424-481 (481)
58 PF00437 T2SE: Type II/IV secr 31.2 1.5E+02 0.0032 22.4 5.3 34 27-60 171-204 (270)
59 TIGR01546 GAPDH-II_archae glyc 30.9 1.4E+02 0.003 24.5 5.3 50 40-92 190-239 (333)
60 PRK04207 glyceraldehyde-3-phos 29.6 2.3E+02 0.0049 22.9 6.4 52 39-93 192-243 (341)
61 PRK10470 ribosome hibernation 28.6 1.7E+02 0.0036 18.9 5.3 34 72-106 60-93 (95)
62 PF14185 SpoIISB_antitox: Anti 28.4 12 0.00025 23.3 -1.0 15 51-65 21-36 (56)
63 cd01760 RBD Ubiquitin-like dom 27.8 99 0.0021 19.7 3.3 21 73-93 12-32 (72)
64 COG1058 CinA Predicted nucleot 27.2 3.2E+02 0.0069 21.7 6.9 61 41-104 192-252 (255)
65 smart00455 RBD Raf-like Ras-bi 27.2 1.5E+02 0.0033 18.5 4.0 23 71-93 10-32 (70)
66 cd00552 RaiA RaiA ("ribosome-a 26.9 1.6E+02 0.0034 18.5 4.2 23 81-103 70-92 (93)
67 COG2061 ACT-domain-containing 26.7 2.8E+02 0.0061 20.9 5.9 51 45-99 100-156 (170)
68 PF00403 HMA: Heavy-metal-asso 26.6 1.4E+02 0.003 17.3 5.9 46 43-93 13-58 (62)
69 PHA02766 hypothetical protein; 26.4 59 0.0013 20.6 2.0 47 30-88 16-62 (73)
70 PF05465 Halo_GVPC: Halobacter 26.3 1.1E+02 0.0023 16.7 2.8 21 86-106 3-23 (32)
71 cd04908 ACT_Bt0572_1 N-termina 25.5 1.5E+02 0.0033 17.4 5.6 45 31-78 4-48 (66)
72 COG5625 Predicted transcriptio 25.3 1.2E+02 0.0026 21.3 3.5 53 42-109 57-111 (113)
73 COG5015 Uncharacterized conser 25.0 50 0.0011 23.9 1.6 29 45-78 48-76 (132)
74 TIGR02538 type_IV_pilB type IV 24.9 1.8E+02 0.0039 25.2 5.3 29 32-60 363-392 (564)
75 PF02196 RBD: Raf-like Ras-bin 24.9 98 0.0021 19.4 2.8 23 71-93 11-33 (71)
76 KOG1521 RNA polymerase I and I 24.4 71 0.0015 26.4 2.6 37 16-52 43-79 (338)
77 PF05986 ADAM_spacer1: ADAM-TS 24.2 2.3E+02 0.005 19.1 5.3 73 4-78 14-100 (114)
78 PRK15197 secreted effector pro 24.1 3.7E+02 0.0079 21.7 6.6 42 56-97 84-132 (291)
79 TIGR00741 yfiA ribosomal subun 23.9 2E+02 0.0043 18.2 5.2 34 72-106 60-93 (95)
80 PHA02781 hypothetical protein; 23.7 68 0.0015 20.7 1.9 26 17-42 6-31 (78)
81 COG0365 Acs Acyl-coenzyme A sy 23.6 4.9E+02 0.011 22.6 7.7 59 35-94 422-483 (528)
82 cd07367 CarBb CarBb is the B s 22.9 1.4E+02 0.0031 23.2 4.0 35 58-99 5-39 (268)
83 COG2033 Desulfoferrodoxin [Ene 22.6 60 0.0013 23.3 1.6 11 59-70 57-67 (126)
84 cd01129 PulE-GspE PulE/GspE Th 22.0 2.7E+02 0.0059 21.5 5.4 29 32-60 127-156 (264)
85 PRK15202 type III secretion ch 22.0 3E+02 0.0064 19.5 9.1 74 13-107 17-114 (117)
86 KOG1521 RNA polymerase I and I 21.8 1.9E+02 0.0042 23.9 4.6 36 69-104 301-336 (338)
87 KOG0758 Mitochondrial carnitin 21.7 1.3E+02 0.0028 24.6 3.6 33 59-92 26-61 (297)
88 PF01933 UPF0052: Uncharacteri 20.3 64 0.0014 25.9 1.6 15 37-51 84-98 (300)
No 1
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=4.9e-45 Score=253.95 Aligned_cols=109 Identities=52% Similarity=0.832 Sum_probs=107.1
Q ss_pred CCCCccccceeeCCCceeeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033831 1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ 80 (110)
Q Consensus 1 mn~p~~~e~~~l~~~~~Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~ 80 (110)
||||+|||+|+|.+|++||++.+|+|++|++.|+|++|||||||+|+.+|+++|+|.||||++|||+++++.|||||+.+
T Consensus 1 MNaP~~fE~fll~eg~kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d 80 (117)
T KOG4392|consen 1 MNAPPAFESFLLFEGEKKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTED 80 (117)
T ss_pred CCCchhhhhheeccCCceeEEecCCCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 033831 81 SSPMQAYNQAINDLDKELDTLKSAFEFLD 109 (110)
Q Consensus 81 ~~p~~al~~a~~~l~~~~~~l~~~f~~a~ 109 (110)
++|.+||.+|+.+++..++.++..|+++-
T Consensus 81 ~~p~~al~~a~~~l~~el~~l~~~f~~~~ 109 (117)
T KOG4392|consen 81 CSPADALTNAITDLIEELSLLENRFKAEA 109 (117)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998753
No 2
>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=1.5e-39 Score=220.61 Aligned_cols=93 Identities=57% Similarity=0.903 Sum_probs=91.3
Q ss_pred CCCceeeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHH
Q 033831 13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92 (110)
Q Consensus 13 ~~~~~Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~ 92 (110)
|+|++||++..+++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|++
T Consensus 1 ~~~~~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~ 80 (93)
T cd06926 1 PEGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAIT 80 (93)
T ss_pred CCCccceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999998999999999999
Q ss_pred HHHHHHHHHHHHh
Q 033831 93 DLDKELDTLKSAF 105 (110)
Q Consensus 93 ~l~~~~~~l~~~f 105 (110)
+|++.|+++++.|
T Consensus 81 ~l~~~~~~~~~~f 93 (93)
T cd06926 81 DLISELSLLKEEF 93 (93)
T ss_pred HHHHHHHHHHhhC
Confidence 9999999999987
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=6.8e-37 Score=201.18 Aligned_cols=77 Identities=47% Similarity=0.788 Sum_probs=72.8
Q ss_pred ceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 033831 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 29 n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f 105 (110)
|+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+++++|.+||++|+++|+++|++|+++|
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 78999999999999999999999999999999999999999999999999999999999999999999999999988
No 4
>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=1.6e-36 Score=202.87 Aligned_cols=82 Identities=32% Similarity=0.575 Sum_probs=79.7
Q ss_pred cCCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033831 24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 24 ~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
..+.+|+++|+|.||||||||+||++|+++|+|.||||+||||+++++.|||||+++.+|.+||++|+++|++.|+++.+
T Consensus 4 ~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~~ 83 (85)
T cd07029 4 EGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILS 83 (85)
T ss_pred ccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999999999999999999999999999999999999899999999999999999999998
Q ss_pred Hh
Q 033831 104 AF 105 (110)
Q Consensus 104 ~f 105 (110)
.|
T Consensus 84 ~f 85 (85)
T cd07029 84 TF 85 (85)
T ss_pred cC
Confidence 87
No 5
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=100.00 E-value=7.1e-36 Score=199.77 Aligned_cols=83 Identities=28% Similarity=0.372 Sum_probs=78.4
Q ss_pred eeccCCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033831 21 YERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT 100 (110)
Q Consensus 21 ~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~ 100 (110)
+...++.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|++.|++
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 33447899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHH
Q 033831 101 LKS 103 (110)
Q Consensus 101 l~~ 103 (110)
|++
T Consensus 83 ~~~ 85 (85)
T PRK01146 83 FLD 85 (85)
T ss_pred HhC
Confidence 863
No 6
>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=2.6e-35 Score=196.29 Aligned_cols=78 Identities=31% Similarity=0.446 Sum_probs=75.9
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033831 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102 (110)
Q Consensus 25 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~ 102 (110)
++.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|++.|++|+
T Consensus 5 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (83)
T cd06927 5 EKEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL 82 (83)
T ss_pred EcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 568899999999999999999999999999999999999999999999999999989999999999999999999986
No 7
>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=5.1e-35 Score=194.88 Aligned_cols=78 Identities=40% Similarity=0.614 Sum_probs=75.4
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033831 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102 (110)
Q Consensus 25 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~ 102 (110)
++.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+|++||++|+++|++.|++|.
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 467899999999999999999999999999999999999999999999999999989999999999999999999985
No 8
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=3.6e-33 Score=191.54 Aligned_cols=90 Identities=37% Similarity=0.552 Sum_probs=86.4
Q ss_pred ceeeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHH
Q 033831 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD 95 (110)
Q Consensus 16 ~~Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~ 95 (110)
.+++++...++.+|+++|++.||||||||+|+++|+++++|+||||+||||+.++++|||||+++++|++||++|++.++
T Consensus 2 ~~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~ 81 (99)
T COG1761 2 TPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKIL 81 (99)
T ss_pred CCceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHHH
Confidence 56788888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHh
Q 033831 96 KELDTLKSAF 105 (110)
Q Consensus 96 ~~~~~l~~~f 105 (110)
+.|++|.++|
T Consensus 82 ~~~~~l~~~~ 91 (99)
T COG1761 82 KDLEELLDQF 91 (99)
T ss_pred HHHHHHHHHH
Confidence 9999999954
No 9
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=99.98 E-value=2.3e-32 Score=187.59 Aligned_cols=83 Identities=31% Similarity=0.586 Sum_probs=80.0
Q ss_pred CCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 033831 26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 26 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f 105 (110)
.+.++.+|++..|||||||.||+.|+++|.|+||||.||||+++++.|||||.++..++++|++||++|+..|+++..+|
T Consensus 13 ~d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF 92 (105)
T KOG3438|consen 13 TDLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKF 92 (105)
T ss_pred cCCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 37789999999999999999999999999999999999999999999999999888999999999999999999999999
Q ss_pred hhh
Q 033831 106 EFL 108 (110)
Q Consensus 106 ~~a 108 (110)
+++
T Consensus 93 ~~~ 95 (105)
T KOG3438|consen 93 EEE 95 (105)
T ss_pred HHH
Confidence 875
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=99.94 E-value=1.4e-26 Score=154.37 Aligned_cols=76 Identities=39% Similarity=0.592 Sum_probs=72.7
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCC------CcceEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q 033831 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDKEL 98 (110)
Q Consensus 25 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl------~~~i~irIqT~~~~~p~~al~~a~~~l~~~~ 98 (110)
++.+|+++|+|.||||||||+||++|++ +.|.||||+||||+ .+++.|+|+|+|+.+|.+||++|++.|.+.|
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 5678999999999999999999999999 99999999999999 9999999999999999999999999999998
Q ss_pred HHH
Q 033831 99 DTL 101 (110)
Q Consensus 99 ~~l 101 (110)
+.|
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=99.71 E-value=1.1e-17 Score=106.17 Aligned_cols=65 Identities=35% Similarity=0.556 Sum_probs=61.1
Q ss_pred eEEEEecCCcchHHHHHHHHhcC-CCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033831 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~ 99 (110)
++|.+.|+|||+||+||..|+++ |+|.+++ ||.++++.++|+|+|+.+|.++|.+|++.|.+.|+
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
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=95.87 E-value=0.043 Score=41.81 Aligned_cols=51 Identities=14% Similarity=0.134 Sum_probs=42.4
Q ss_pred CCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 53 DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 53 ~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
.| |. |.|+..- .++..+.|.|+|.++|.+|+..|++-|.+.++.|.+..+.
T Consensus 138 ~p-vd-a~y~~~~--~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~ 188 (195)
T PRK14979 138 QP-CN-AVYKQIS--NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEG 188 (195)
T ss_pred cc-ee-eEEecCC--CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45 44 5565332 5999999999999999999999999999999999887754
No 13
>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=95.65 E-value=0.025 Score=43.26 Aligned_cols=46 Identities=26% Similarity=0.236 Sum_probs=37.9
Q ss_pred CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033831 55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT 100 (110)
Q Consensus 55 ~V~fAgY~vpH------Pl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~ 100 (110)
=|.-+.|.|.- .-.+++.|-|.|+|.++|.+||..|++.|.+.+.-
T Consensus 163 PV~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~~ 214 (215)
T cd06928 163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSP 214 (215)
T ss_pred CeEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhhc
Confidence 36777788643 34578999999999999999999999999988753
No 14
>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=95.54 E-value=0.046 Score=41.92 Aligned_cols=52 Identities=17% Similarity=0.262 Sum_probs=44.0
Q ss_pred hcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033831 51 HRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 51 ~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
-+-.=|.-|+|++. |-.++..|.|-|+|..+|.+|+.+|++-|+..++.|.+
T Consensus 160 Ak~sPV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~ 211 (212)
T cd07028 160 AKFGPVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL 211 (212)
T ss_pred CEeCCceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence 34445677889863 36799999999999999999999999999999998875
No 15
>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=95.24 E-value=0.064 Score=42.97 Aligned_cols=49 Identities=24% Similarity=0.310 Sum_probs=40.4
Q ss_pred CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033831 55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 55 ~V~fAgY~vpH------Pl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
-|.-+.|.|.. ...+++.+.|.|+|.++|.+||.+|++-|...|..|.+
T Consensus 154 PV~~Vny~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 154 PVLKVNYEVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred CeEEEEEEEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 35667777653 23478999999999999999999999999999988854
No 16
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=95.21 E-value=0.045 Score=41.92 Aligned_cols=45 Identities=24% Similarity=0.313 Sum_probs=37.6
Q ss_pred eeeeeeeCCCCC----------------CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033831 56 VLFAGYKLPHPL----------------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT 100 (110)
Q Consensus 56 V~fAgY~vpHPl----------------~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~ 100 (110)
|..+.|.+.-|. .+++.|.|.|+|..+|.+||.+|++-|...++.
T Consensus 163 v~~v~~~~~~~~~~~~~~~~~~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~ 223 (224)
T smart00662 163 VDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 223 (224)
T ss_pred hhheeeeccCCccceecccchhhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence 455667666654 588999999999999999999999999988764
No 17
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=94.78 E-value=0.029 Score=43.64 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=28.9
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcC-CC
Q 033831 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN 55 (110)
Q Consensus 18 Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~ 55 (110)
++++.+ ...+.++|.+.|-++|+||+||..|+.. |.
T Consensus 2 ~~~~~~--~~~~~~~f~~~g~~~t~~NalRRvlls~vp~ 38 (263)
T PRK00783 2 EIEILE--LDDRSARFVVEGVTPAFANAIRRAMIADVPT 38 (263)
T ss_pred ceEEEE--cCCcEEEEEEeCCCHHHHHHHHHHHHHcCCe
Confidence 345554 3558899999999999999999999874 54
No 18
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=94.61 E-value=0.094 Score=42.74 Aligned_cols=49 Identities=18% Similarity=0.169 Sum_probs=41.0
Q ss_pred CeeeeeeeCCCC-----CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033831 55 NVLFAGYKLPHP-----LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 55 ~V~fAgY~vpHP-----l~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
=|.-+.|.|..- ..+++.|-|.|+|.++|.+||..|++.|.+.+..|.+
T Consensus 170 PV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~ 223 (327)
T CHL00013 170 PVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH 223 (327)
T ss_pred CeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 366777887641 2578999999999999999999999999999987753
No 19
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=94.61 E-value=0.11 Score=42.00 Aligned_cols=48 Identities=21% Similarity=0.243 Sum_probs=40.1
Q ss_pred eeeeeeeCCCC------CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033831 56 VLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 56 V~fAgY~vpHP------l~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
|.-+.|.+.-. -.+++.+.|.|+|.++|.+||.+|++.|+..+..|.+
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 66677876542 1468999999999999999999999999999988754
No 20
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=94.24 E-value=0.096 Score=42.70 Aligned_cols=47 Identities=26% Similarity=0.262 Sum_probs=37.9
Q ss_pred eEeeccCCCcceeEEEE----ecCCcchHHHHHHHHhc-CCCeeeeeeeCCC
Q 033831 19 VSYERDTKIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH 65 (110)
Q Consensus 19 v~~~~~~~~~n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~vpH 65 (110)
+++...+...+.+.|.| .|..|||||+||..|+. .|+..+.+-++.+
T Consensus 10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 55566677789999999 67889999999999988 5887777767654
No 21
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=93.83 E-value=0.15 Score=41.11 Aligned_cols=47 Identities=26% Similarity=0.280 Sum_probs=35.3
Q ss_pred eeEeeccCCCcceeEEEEe----cCCcchHHHHHHHHhc-CCCeeeeeeeCC
Q 033831 18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHR-DENVLFAGYKLP 64 (110)
Q Consensus 18 Kv~~~~~~~~~n~~~~~i~----~EDHTLgNlLr~~L~~-~~~V~fAgY~vp 64 (110)
++++...+..++.+.|.|. |.++|+||+||..|+. .|+.-.-+-++.
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 3444443335789999996 9999999999999987 477666666653
No 22
>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=93.83 E-value=0.07 Score=40.90 Aligned_cols=33 Identities=12% Similarity=0.190 Sum_probs=28.3
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHHhcC-CCee
Q 033831 25 TKIINAASFTIEREEHTIGNILRMQLHRD-ENVL 57 (110)
Q Consensus 25 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~ 57 (110)
++.++.+.|.+.|-|+|+||+||..|+.. |..-
T Consensus 7 ~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~A 40 (212)
T cd07028 7 EADKDNVDFILSGVDLAMANALRRVMIAEVPTMA 40 (212)
T ss_pred EcCCCEEEEEEEccChhHHHHHHHHHHHcCcceE
Confidence 46788999999999999999999999874 5533
No 23
>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=93.75 E-value=0.067 Score=41.51 Aligned_cols=36 Identities=14% Similarity=0.167 Sum_probs=29.0
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcC-CC
Q 033831 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN 55 (110)
Q Consensus 18 Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~ 55 (110)
+|++.+ ..++.+.|.+.|-|+|+||+||..|+.. |.
T Consensus 2 ~~~~~~--~~~~~~~f~~~g~~~s~~NalRRills~vp~ 38 (259)
T cd07030 2 EIEVLE--LDDDRARFVLEGVPPAFANAIRRAIISEVPT 38 (259)
T ss_pred ceEEEe--cCCCEEEEEEeCCCHHHHHHHHHHHHhcCCe
Confidence 345554 4568899999999999999999999874 54
No 24
>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=93.53 E-value=0.17 Score=39.93 Aligned_cols=40 Identities=20% Similarity=0.210 Sum_probs=37.2
Q ss_pred CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 68 ~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
.+++.+.|-|+|..+|.++|.+|++-|.+.++.|.+..+.
T Consensus 225 ~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~ 264 (265)
T cd07031 225 PDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264 (265)
T ss_pred CCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5789999999999999999999999999999999988764
No 25
>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=93.38 E-value=0.13 Score=39.29 Aligned_cols=40 Identities=28% Similarity=0.294 Sum_probs=31.3
Q ss_pred CCCcceeEEEE----ecCCcchHHHHHHHHhc-CCCeeeeeeeCC
Q 033831 25 TKIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLP 64 (110)
Q Consensus 25 ~~~~n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~vp 64 (110)
+...+.+.|.| .|.++|+||+||..|+. .|+.-.-+-++.
T Consensus 5 ~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~ 49 (215)
T cd06928 5 NKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE 49 (215)
T ss_pred cCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence 34568899999 78999999999999987 476655555543
No 26
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=92.74 E-value=0.23 Score=37.81 Aligned_cols=40 Identities=13% Similarity=0.147 Sum_probs=31.8
Q ss_pred EeeccCCCcceeEEEEecCCcchHHHHHHHHhc-CCCeeeee
Q 033831 20 SYERDTKIINAASFTIEREEHTIGNILRMQLHR-DENVLFAG 60 (110)
Q Consensus 20 ~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~-~~~V~fAg 60 (110)
+++.-+|..+.+.|.+. -+.|+||+||..|+. .|+.-.-+
T Consensus 5 ~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~ 45 (195)
T PRK14979 5 KEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN 45 (195)
T ss_pred ceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence 34444788999999999 999999999999987 46644444
No 27
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=92.02 E-value=0.35 Score=39.27 Aligned_cols=45 Identities=18% Similarity=0.017 Sum_probs=32.6
Q ss_pred eEeeccC--CCcceeEEEEecCCcchHHHHHHHHhc-CCCeeeeeeeC
Q 033831 19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHR-DENVLFAGYKL 63 (110)
Q Consensus 19 v~~~~~~--~~~n~~~~~i~~EDHTLgNlLr~~L~~-~~~V~fAgY~v 63 (110)
|++...+ ..+-.+++...|-+|||||+||..|+. .|+.-.-+-+|
T Consensus 7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I 54 (317)
T COG0202 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEI 54 (317)
T ss_pred eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEE
Confidence 4444433 347788999999999999999999987 57654444333
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=92.01 E-value=0.4 Score=37.80 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=31.3
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHHhc-CCCeeeee
Q 033831 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHR-DENVLFAG 60 (110)
Q Consensus 18 Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~-~~~V~fAg 60 (110)
+|++.+ ..++.++|.+.+=|+|+||+||..|+. .|..-.-.
T Consensus 2 ~i~i~~--~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~ 43 (265)
T cd07031 2 RVEITE--LTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDL 43 (265)
T ss_pred cEEEEE--cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEE
Confidence 345554 456889999999999999999999987 46544333
No 29
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=91.05 E-value=0.33 Score=37.13 Aligned_cols=33 Identities=24% Similarity=0.264 Sum_probs=26.3
Q ss_pred eEEEEecCCcchHHHHHHHHhc-CCCeeeeeeeC
Q 033831 31 ASFTIEREEHTIGNILRMQLHR-DENVLFAGYKL 63 (110)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~-~~~V~fAgY~v 63 (110)
+.|.+.+-++|+||+||..|+. .|+.-.-+.++
T Consensus 2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I 35 (224)
T smart00662 2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI 35 (224)
T ss_pred eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence 6799999999999999999987 46655555444
No 30
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=89.07 E-value=1.2 Score=34.64 Aligned_cols=41 Identities=20% Similarity=0.199 Sum_probs=37.4
Q ss_pred CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 67 l~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
..++..+.|.|+|..+|.+++..|++-|.+.++.|.+..+.
T Consensus 221 ~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~~~~ 261 (263)
T PRK00783 221 DENKFIFTVESDGSLPVEEILLEALKILKRKADELIEALEE 261 (263)
T ss_pred cCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 46778899999999999999999999999999999988765
No 31
>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=86.61 E-value=2 Score=33.31 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=33.5
Q ss_pred CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033831 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (110)
Q Consensus 68 ~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~ 104 (110)
.+...+.|.|.|..+|.+++++|++-|.+.++.|.++
T Consensus 222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~ 258 (259)
T cd07030 222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258 (259)
T ss_pred CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4567889999999999999999999999999999765
No 32
>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=85.44 E-value=1.1 Score=35.96 Aligned_cols=29 Identities=24% Similarity=0.187 Sum_probs=23.5
Q ss_pred ecCCcchHHHHHHHHhc-CCCeeeeeeeCC
Q 033831 36 EREEHTIGNILRMQLHR-DENVLFAGYKLP 64 (110)
Q Consensus 36 ~~EDHTLgNlLr~~L~~-~~~V~fAgY~vp 64 (110)
.|.+|||||+||..|+. .|++-..+-++.
T Consensus 11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~ 40 (297)
T TIGR02027 11 RGFGITLGNALRRVLLSSIPGAAITAVKID 40 (297)
T ss_pred CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence 58899999999999988 577766666654
No 33
>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=85.04 E-value=2.4 Score=34.10 Aligned_cols=37 Identities=22% Similarity=0.266 Sum_probs=34.0
Q ss_pred CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033831 67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 67 l~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
-.+.+.+.|-++|..+|.+.|.+|++-|.+.|+.|.+
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 4677999999999999999999999999999999875
No 34
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=70.80 E-value=5.2 Score=28.38 Aligned_cols=37 Identities=16% Similarity=0.143 Sum_probs=29.5
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCC
Q 033831 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLP 64 (110)
Q Consensus 28 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~vp 64 (110)
+..+..++.+|.|++|..+-..+++..+ |.+-|..+|
T Consensus 4 ~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp 42 (137)
T PRK02261 4 KTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTS 42 (137)
T ss_pred CEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCC
Confidence 3456788999999999999999999866 666666665
No 35
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=69.81 E-value=2.9 Score=34.57 Aligned_cols=26 Identities=31% Similarity=0.613 Sum_probs=23.1
Q ss_pred EecCCcchHHHHHHHHhcCCCeeeee
Q 033831 35 IEREEHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 35 i~~EDHTLgNlLr~~L~~~~~V~fAg 60 (110)
+..-.|++.|.||..|.+||+|.+.|
T Consensus 180 vG~dT~sF~~aLraALReDPDVIlvG 205 (353)
T COG2805 180 VGRDTLSFANALRAALREDPDVILVG 205 (353)
T ss_pred hcccHHHHHHHHHHHhhcCCCEEEEe
Confidence 34457899999999999999999998
No 36
>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=66.04 E-value=13 Score=27.49 Aligned_cols=38 Identities=24% Similarity=0.300 Sum_probs=30.2
Q ss_pred ceeEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCCCC
Q 033831 29 NAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (110)
Q Consensus 29 n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~vpHP 66 (110)
.-+..++.||.|+||-.+...+++..+ |.+.|-.+|+.
T Consensus 84 ~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~ 123 (201)
T cd02070 84 KVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPE 123 (201)
T ss_pred eEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHH
Confidence 446678899999999999998888765 66677777765
No 37
>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=65.60 E-value=19 Score=24.46 Aligned_cols=25 Identities=16% Similarity=0.090 Sum_probs=22.3
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCC
Q 033831 31 ASFTIEREEHTIGNILRMQLHRDEN 55 (110)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~~~ 55 (110)
+..++.+|.|++|..+-..+++..+
T Consensus 3 v~~~~~gd~H~lG~~~~~~~l~~~G 27 (122)
T cd02071 3 LVAKPGLDGHDRGAKVIARALRDAG 27 (122)
T ss_pred EEEecCCChhHHHHHHHHHHHHHCC
Confidence 5678899999999999999999866
No 38
>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=65.23 E-value=18 Score=24.04 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=25.6
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCC
Q 033831 31 ASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLP 64 (110)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~vp 64 (110)
+...+.+|.|++|..+-..+++..+ |.+.|-.+|
T Consensus 3 l~~~~~~e~H~lG~~~~~~~l~~~G~~V~~lg~~~~ 38 (119)
T cd02067 3 VIATVGGDGHDIGKNIVARALRDAGFEVIDLGVDVP 38 (119)
T ss_pred EEEeeCCchhhHHHHHHHHHHHHCCCEEEECCCCCC
Confidence 4567899999999999999998766 434454444
No 39
>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=60.50 E-value=38 Score=20.99 Aligned_cols=68 Identities=13% Similarity=0.164 Sum_probs=36.0
Q ss_pred eeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCC-CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033831 30 AASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL-QYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 30 ~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl-~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~ 99 (110)
++.|++.++-=+|..+|...-..+=++.-- -..|++- .....++|++++..+ .+.++++++.|...+.
T Consensus 3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i-~s~p~~~~~~~~~f~vd~~~~~~-~~~~~~~l~~l~~~~~ 71 (80)
T cd04905 3 SIVFTLPNKPGALYDVLGVFAERGINLTKI-ESRPSKGGLWEYVFFIDFEGHIE-DPNVAEALEELKRLTE 71 (80)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCcCEEEE-EEEEcCCCCceEEEEEEEECCCC-CHHHHHHHHHHHHhCC
Confidence 345555544334444443322222222211 2334432 456889999987533 4777888877776554
No 40
>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=59.59 E-value=11 Score=27.93 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=31.7
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCCCC
Q 033831 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (110)
Q Consensus 28 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~vpHP 66 (110)
+.-+..++.||.|.||..+...+++..+ |.|.|-.+|-.
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e 125 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPID 125 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHH
Confidence 3456788899999999999999999865 77778777744
No 41
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=58.04 E-value=20 Score=29.12 Aligned_cols=40 Identities=15% Similarity=0.057 Sum_probs=35.8
Q ss_pred CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 68 ~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
.++..+.+-|++.+.|.+|+..|.+-+.+.|+.+.+.+..
T Consensus 187 ~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~ 226 (317)
T COG0202 187 KDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPK 226 (317)
T ss_pred ceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3778888999999999999999999999999999887764
No 42
>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=57.54 E-value=12 Score=28.29 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=31.5
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCC--eeeeeeeCCCC
Q 033831 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (110)
Q Consensus 28 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~vpHP 66 (110)
...+..++.||.|.||-.+...+++..+ |.+-|-++|-+
T Consensus 89 ~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e 129 (213)
T cd02069 89 GKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIE 129 (213)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHH
Confidence 3456788899999999999999999866 77777777644
No 43
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.29 E-value=59 Score=26.20 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=39.8
Q ss_pred cchHHHHHHHHhc-CCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHH
Q 033831 40 HTIGNILRMQLHR-DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92 (110)
Q Consensus 40 HTLgNlLr~~L~~-~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~ 92 (110)
-++-|.|+...-+ -+.|+|+-|.+-||.-=-+.+..-|+.......+++.+++
T Consensus 92 d~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~n 145 (276)
T KOG2972|consen 92 DGIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIFN 145 (276)
T ss_pred HHHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHHH
Confidence 3678999998876 5889999999999999888888888754333344444443
No 44
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=43.84 E-value=57 Score=26.26 Aligned_cols=64 Identities=19% Similarity=0.122 Sum_probs=49.9
Q ss_pred HHHHHHHh--------cCCCeeeeeeeCCCC---------CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033831 44 NILRMQLH--------RDENVLFAGYKLPHP---------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 44 NlLr~~L~--------~~~~V~fAgY~vpHP---------l~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
|.||+.+. +-|++..++|.-+-| --+++++.|...|+..|...+..|++-|.+.++.|.....
T Consensus 187 n~lrhT~y~~e~~~~~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~ 266 (285)
T KOG1522|consen 187 NKLRHTLYWFEEDDLIEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALS 266 (285)
T ss_pred HhhhccCCCccccchhhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 77776663 447788888776511 1278999999999999999999999999999998877654
Q ss_pred h
Q 033831 107 F 107 (110)
Q Consensus 107 ~ 107 (110)
.
T Consensus 267 ~ 267 (285)
T KOG1522|consen 267 T 267 (285)
T ss_pred c
Confidence 3
No 45
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=41.10 E-value=31 Score=28.28 Aligned_cols=98 Identities=23% Similarity=0.255 Sum_probs=53.7
Q ss_pred CCCCccccceeeCCCceeeEeeccCCCcceeEEEEecCCcchHHHHHHHH---hcCCCeeee---------eeeCCCCCC
Q 033831 1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQL---HRDENVLFA---------GYKLPHPLQ 68 (110)
Q Consensus 1 mn~p~~~e~~~l~~~~~Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L---~~~~~V~fA---------gY~vpHPl~ 68 (110)
||+||.||.=-||+......-..+.....++. .--=....+..... +.-.+|.|. ||+.. .
T Consensus 4 ~~~pDvYET~dl~~~~~~~~~~~~~~~~~~I~----~~~l~~~~A~~kF~~~~vda~~vDFSd~i~~krr~~~~~~---~ 76 (388)
T PF04912_consen 4 YDAPDVYETPDLPEDVQTSSDDDDEDESEDIE----RSRLNPDEARSKFKGARVDARGVDFSDRISKKRRSGYRSR---S 76 (388)
T ss_pred CCCCCCcCCCCCCccccccCCCCccccccchh----hcCCCHHHHHHHhCcCcCCCCCCCchhhcccccccccccC---C
Confidence 69999999999999887654222222211211 11111222222222 234677776 34443 1
Q ss_pred cceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033831 69 YKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEFL 108 (110)
Q Consensus 69 ~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~a 108 (110)
+... +--+ +.+..+-+.+=+.+|..++++|++.+.+.
T Consensus 77 ~~~e--~~g~-~~~e~Es~~~kl~RL~~Ev~EL~eEl~~~ 113 (388)
T PF04912_consen 77 GEYE--ILGD-DSSEKESPEQKLQRLRREVEELKEELEKR 113 (388)
T ss_pred Ccee--ecCC-CCCCcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 1112 1111 12345667788899999999998888663
No 46
>PRK00549 competence damage-inducible protein A; Provisional
Probab=40.96 E-value=1.3e+02 Score=25.05 Aligned_cols=54 Identities=19% Similarity=0.346 Sum_probs=34.4
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033831 40 HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 40 HTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~ 99 (110)
=.|...|...+...++|.++.| || ...+.+|+...+. + .+..++.++.+.+.+.
T Consensus 191 s~l~~~L~~l~~~~~~v~ig~~--~~--~~~~~vrl~~~~~-~-~~~~~~~~~~~~~~i~ 244 (414)
T PRK00549 191 SQLATTLRDLIDNQTNPTIAPY--AK--DGEVTLRLTAKAR-S-EEEAEKLIDPLEEEIR 244 (414)
T ss_pred HHHHHHHHHHHhcCCCCEEEEC--cc--CCEEEEEEEEecC-C-HHHHHHHHHHHHHHHH
Confidence 4577788777777889998866 33 4668888887654 3 3444555554444443
No 47
>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=40.35 E-value=79 Score=20.51 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 79 SQSSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 79 ~~~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
+..+|.++|..-+..|.+++.++.-.+..
T Consensus 7 ~s~~p~~~Ls~vl~~LqDE~~hm~~e~~~ 35 (79)
T PF06657_consen 7 PSQSPGEALSEVLKALQDEFGHMKMEHQE 35 (79)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999999877654
No 48
>PLN02231 alanine transaminase
Probab=37.74 E-value=1.5e+02 Score=25.38 Aligned_cols=58 Identities=7% Similarity=-0.026 Sum_probs=40.1
Q ss_pred HHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033831 46 LRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 46 Lr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
+...|++..+|.+.--..-.+....-.||+..- .+.+.+++|+++|...++.+.++|+
T Consensus 476 ~~~~Ll~~~GV~vvPGs~Fg~~~g~~~~Rit~~---~~~e~l~eal~RL~~~~~~~~~~~~ 533 (534)
T PLN02231 476 YCKRLLNATGIVVVPGSGFGQVPGTWHFRCTIL---PQEDKIPAIVSRLTEFHKSFMDEFR 533 (534)
T ss_pred HHHHHHHhcCEEEeCCcccCCCCCCCeEEEEeC---CCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 455566666766553332233344556777652 4679999999999999999998886
No 49
>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=36.84 E-value=45 Score=26.89 Aligned_cols=34 Identities=18% Similarity=0.174 Sum_probs=27.9
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 033831 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (110)
Q Consensus 18 Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~ 53 (110)
||++.+ ..++.++|.+.|-|=.+.|+||..|+..
T Consensus 2 ~i~i~~--~~~~~~~f~l~~~d~s~ANAlRRimiaE 35 (291)
T cd07032 2 KIEIIS--LSDEELEFDLIGVDASIANAFRRILLAE 35 (291)
T ss_pred eEEEEE--CCCCEEEEEEecCCHHHHHHHHHHHHhc
Confidence 345543 5668999999999999999999998763
No 50
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=34.93 E-value=34 Score=29.77 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=23.0
Q ss_pred ecCCcchHHHHHHHHhcCCCeeeee
Q 033831 36 EREEHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 36 ~~EDHTLgNlLr~~L~~~~~V~fAg 60 (110)
.+-+-|+.++||..|.+||+|.+.|
T Consensus 310 ~k~gltfa~~LRa~LRqDPDvImVG 334 (500)
T COG2804 310 PKIGLTFARALRAILRQDPDVIMVG 334 (500)
T ss_pred cccCCCHHHHHHHHhccCCCeEEEe
Confidence 4568899999999999999999998
No 51
>PRK01215 competence damage-inducible protein A; Provisional
Probab=34.55 E-value=2.3e+02 Score=22.24 Aligned_cols=45 Identities=16% Similarity=0.270 Sum_probs=27.2
Q ss_pred EEEEecC-CcchHHHHHHHHhcCCCeee--e--eeeCCCCCCcceEEEEEeCC
Q 033831 32 SFTIERE-EHTIGNILRMQLHRDENVLF--A--GYKLPHPLQYKIIVRIHTTS 79 (110)
Q Consensus 32 ~~~i~~E-DHTLgNlLr~~L~~~~~V~f--A--gY~vpHPl~~~i~irIqT~~ 79 (110)
++.+.|- -=+|.-.|.....+.|+|.+ + ||. +|+ ..+.+|+..++
T Consensus 183 ~~~~~Gi~Es~l~~~l~~l~~~~~~~~~~s~p~~~~-~~~--~~v~vrl~~~~ 232 (264)
T PRK01215 183 SILVEGVMESDLAPYVKELVKKYDRVYVKSHPKGYE-VSK--PILEIQIAGSG 232 (264)
T ss_pred EEEECCCCHHHHHHHHHHHHHhCCCCEEecCcccee-cCC--CeEEEEEEEec
Confidence 3445442 23566667666667788887 3 244 343 56788887664
No 52
>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=34.49 E-value=61 Score=20.36 Aligned_cols=24 Identities=13% Similarity=0.194 Sum_probs=16.5
Q ss_pred eEEEEEeCCCCCHHHHHHHHHHHH
Q 033831 71 IIVRIHTTSQSSPMQAYNQAINDL 94 (110)
Q Consensus 71 i~irIqT~~~~~p~~al~~a~~~l 94 (110)
-..+|+++++.+-.++|++||+..
T Consensus 7 rr~~vkvtp~~~l~~VL~eac~k~ 30 (65)
T PF11470_consen 7 RRFKVKVTPNTTLNQVLEEACKKF 30 (65)
T ss_dssp -EEEE---TTSBHHHHHHHHHHHT
T ss_pred cEEEEEECCCCCHHHHHHHHHHHc
Confidence 356788888888899999999754
No 53
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=34.37 E-value=1.2e+02 Score=21.71 Aligned_cols=15 Identities=20% Similarity=0.293 Sum_probs=8.7
Q ss_pred CHHHHHHHHHHHHHH
Q 033831 82 SPMQAYNQAINDLDK 96 (110)
Q Consensus 82 ~p~~al~~a~~~l~~ 96 (110)
+=-++|++|++++-.
T Consensus 57 sF~d~Lk~Al~~VN~ 71 (127)
T PRK12729 57 SFSEAMKNALTSVND 71 (127)
T ss_pred CHHHHHHHHHHHHHH
Confidence 335667777665543
No 54
>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=34.17 E-value=31 Score=20.17 Aligned_cols=24 Identities=21% Similarity=0.122 Sum_probs=10.9
Q ss_pred eeEeeccCCCcceeEEEEecCCcch
Q 033831 18 KVSYERDTKIINAASFTIEREEHTI 42 (110)
Q Consensus 18 Kv~~~~~~~~~n~~~~~i~~EDHTL 42 (110)
++++.-.+.. ..+++.+.|+.+||
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 3444444444 67888899998886
No 55
>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=34.01 E-value=97 Score=19.58 Aligned_cols=33 Identities=15% Similarity=0.351 Sum_probs=25.2
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 033831 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 72 ~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f 105 (110)
.|++...+ .+...||..|++.|...+...+++.
T Consensus 62 ~l~a~~~~-~d~~~Aid~a~dkl~rql~k~k~k~ 94 (97)
T PF02482_consen 62 VLVAEESA-EDLYAAIDEAFDKLERQLRKYKEKL 94 (97)
T ss_dssp EEEEEEEE-SSHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred eEEEEEec-CCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44444443 3899999999999999998877654
No 56
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=32.60 E-value=1.7e+02 Score=20.19 Aligned_cols=27 Identities=22% Similarity=0.298 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 81 SSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 81 ~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
-++..||..|++.|...+.-.+++.+.
T Consensus 70 ~d~YaAID~a~dKLerqlrK~K~K~~~ 96 (110)
T COG1544 70 EDMYAAIDLAIDKLERQLRKHKEKLKD 96 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 389999999999999999998888765
No 57
>PTZ00377 alanine aminotransferase; Provisional
Probab=31.46 E-value=2.2e+02 Score=23.59 Aligned_cols=58 Identities=7% Similarity=0.080 Sum_probs=38.2
Q ss_pred HHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033831 46 LRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 46 Lr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
+...+++..+|.+.....-.+....-.+|+-.. .+.+.+++|+++|.+.++.+.++|.
T Consensus 424 ~~~~ll~~~gV~v~pG~~F~~~~~~~~~Rls~~---~~~e~l~~~l~rl~~~~~~~~~~~~ 481 (481)
T PTZ00377 424 YCLELLESTGIVVVPGSGFGQKPGTYHFRITIL---PPEEQIEEMVKKIKEFHESFMKKYG 481 (481)
T ss_pred HHHHHHHHcCEEEeCCcccCCCCCCCEEEEEEC---CCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 344566666776653332222222346888764 3468999999999999998888773
No 58
>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=31.22 E-value=1.5e+02 Score=22.40 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=26.5
Q ss_pred CcceeEEEEecCCcchHHHHHHHHhcCCCeeeee
Q 033831 27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 27 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAg 60 (110)
.++...+.-....+++..+|+..|..+|++.+.|
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 4566666656789999999999999999998877
No 59
>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=30.91 E-value=1.4e+02 Score=24.50 Aligned_cols=50 Identities=8% Similarity=0.120 Sum_probs=39.7
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHH
Q 033831 40 HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92 (110)
Q Consensus 40 HTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~ 92 (110)
|| |-.+...|=... +.=.+.+||.|+-+-.-+.++++..++. +-+.++++
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 888988887666 7788899999999999999999887654 44444443
No 60
>PRK04207 glyceraldehyde-3-phosphate dehydrogenase; Provisional
Probab=29.58 E-value=2.3e+02 Score=22.87 Aligned_cols=52 Identities=15% Similarity=0.197 Sum_probs=38.1
Q ss_pred CcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHH
Q 033831 39 EHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 39 DHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~ 93 (110)
.|+ |.-++..|-.. .|.-...+||-+.-+-.-+.++++..++. +.+.+++++
T Consensus 192 ~~~-g~~v~~vlp~l-~i~~~avrVPv~~gh~~~v~v~l~~~~t~-eev~~~l~~ 243 (341)
T PRK04207 192 SHH-GPDVKTVLPDL-DITTMAVKVPTTLMHMHSVNVELKKPVTK-EEVLEALEN 243 (341)
T ss_pred CCc-hhHHHhhCCCC-ceEEEEEEcCCCCceEEEEEEEECCCCCH-HHHHHHHHh
Confidence 355 76777666222 38888899999999999999999987765 555555543
No 61
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=28.56 E-value=1.7e+02 Score=18.86 Aligned_cols=34 Identities=18% Similarity=0.261 Sum_probs=27.4
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033831 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 72 ~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
.++++..+. +...|+..|++.|...+...++...
T Consensus 60 ~l~a~~~~~-d~y~Aid~a~~klerqL~k~k~k~~ 93 (95)
T PRK10470 60 EIHASAEGQ-DMYAAIDGLIDKLARQLTKHKDKLK 93 (95)
T ss_pred EEEEEEecC-cHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 566666544 8999999999999999988887654
No 62
>PF14185 SpoIISB_antitox: Antitoxin SpoIISB, type II toxin-antitoxin system ; PDB: 3O6Q_B.
Probab=28.42 E-value=12 Score=23.30 Aligned_cols=15 Identities=40% Similarity=0.789 Sum_probs=5.0
Q ss_pred hcCCCeeeeeeeC-CC
Q 033831 51 HRDENVLFAGYKL-PH 65 (110)
Q Consensus 51 ~~~~~V~fAgY~v-pH 65 (110)
.+-..|.||+|.| ||
T Consensus 21 Kk~s~~s~a~y~vSPh 36 (56)
T PF14185_consen 21 KKKSYTSFAEYKVSPH 36 (56)
T ss_dssp E---SEEE------HH
T ss_pred HHhhhccccccccChH
Confidence 4456789999987 55
No 63
>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=27.84 E-value=99 Score=19.70 Aligned_cols=21 Identities=10% Similarity=0.023 Sum_probs=17.0
Q ss_pred EEEEeCCCCCHHHHHHHHHHH
Q 033831 73 VRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 73 irIqT~~~~~p~~al~~a~~~ 93 (110)
-.|++.+|.+..++|.++|+.
T Consensus 12 t~V~vrpg~ti~d~L~~~c~k 32 (72)
T cd01760 12 TVVPVRPGMSVRDVLAKACKK 32 (72)
T ss_pred EEEEECCCCCHHHHHHHHHHH
Confidence 346667888999999999974
No 64
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=27.21 E-value=3.2e+02 Score=21.66 Aligned_cols=61 Identities=13% Similarity=0.165 Sum_probs=38.6
Q ss_pred chHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033831 41 TIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (110)
Q Consensus 41 TLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~ 104 (110)
.|.-.|.......++|.++.|--..-.... .|.|+... .-.++++.+++.+...+......
T Consensus 192 ~la~~L~~i~~~~~~~~i~s~p~~~~~~~~-~~~i~~~~--~~~~~~~~~~~~~~~~i~~~~~~ 252 (255)
T COG1058 192 SLAPTLKDLQDEQPNVTIASYPKDGEVRLR-ELVIRAEA--RDEEEADALLRWLEGRLRARGAE 252 (255)
T ss_pred HHHHHHHHHHhcCCCCEEEecCCCCceecc-ceEEEEec--CCHHHHHHHHHHHHHHHHHhhhh
Confidence 577788888888899988876544332221 33366543 23577777777777766655443
No 65
>smart00455 RBD Raf-like Ras-binding domain.
Probab=27.16 E-value=1.5e+02 Score=18.53 Aligned_cols=23 Identities=9% Similarity=0.085 Sum_probs=18.4
Q ss_pred eEEEEEeCCCCCHHHHHHHHHHH
Q 033831 71 IIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 71 i~irIqT~~~~~p~~al~~a~~~ 93 (110)
-...|+.+++.+..++|..+|+.
T Consensus 10 ~~~~V~vrpg~tl~e~L~~~~~k 32 (70)
T smart00455 10 QRTVVKVRPGKTVRDALAKALKK 32 (70)
T ss_pred CEEEEEECCCCCHHHHHHHHHHH
Confidence 44567777888999999999874
No 66
>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=26.93 E-value=1.6e+02 Score=18.50 Aligned_cols=23 Identities=22% Similarity=0.390 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q 033831 81 SSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 81 ~~p~~al~~a~~~l~~~~~~l~~ 103 (110)
.+...||..|++.|...+...++
T Consensus 70 ~d~~~Aid~a~~kl~rqL~k~k~ 92 (93)
T cd00552 70 EDLYAAIDLAVDKLERQLRKYKE 92 (93)
T ss_pred CCHHHHHHHHHHHHHHHHHHhcc
Confidence 48899999999999988876653
No 67
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=26.65 E-value=2.8e+02 Score=20.85 Aligned_cols=51 Identities=10% Similarity=0.067 Sum_probs=35.4
Q ss_pred HHHHHHhcCCCee-----eeeeeCCCC-CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033831 45 ILRMQLHRDENVL-----FAGYKLPHP-LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 45 lLr~~L~~~~~V~-----fAgY~vpHP-l~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~ 99 (110)
=++..+-+...+- =-.-++||| .++...|++...+ .+.+++|+..+...|.
T Consensus 100 diqDTId~In~ig~A~vvDl~L~Mp~~e~~SsA~iti~a~~----~e~l~ea~~~l~ev~~ 156 (170)
T COG2061 100 DIQDTIDRINSIGGAEVVDLSLSMPGIEGESSARITIIAVG----KEKLDEALRRLKEVAM 156 (170)
T ss_pred cHHHHHHHhhccCCEEEEEEEeecCCCCCCcceeEEEEEcC----hhHHHHHHHHHHHHHh
Confidence 4555555544333 345789999 5888899998865 4788888888776654
No 68
>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=26.59 E-value=1.4e+02 Score=17.25 Aligned_cols=46 Identities=15% Similarity=0.108 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHH
Q 033831 43 GNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 43 gNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~ 93 (110)
.+.++..|.+.|+|.-+-.... .+.+.+....+. .++ +.+.+++++
T Consensus 13 ~~~v~~~l~~~~GV~~v~vd~~---~~~v~v~~~~~~-~~~-~~i~~~i~~ 58 (62)
T PF00403_consen 13 AKKVEKALSKLPGVKSVKVDLE---TKTVTVTYDPDK-TSI-EKIIEAIEK 58 (62)
T ss_dssp HHHHHHHHHTSTTEEEEEEETT---TTEEEEEESTTT-SCH-HHHHHHHHH
T ss_pred HHHHHHHHhcCCCCcEEEEECC---CCEEEEEEecCC-CCH-HHHHHHHHH
Confidence 4678889999999977766654 344554443332 344 777777765
No 69
>PHA02766 hypothetical protein; Provisional
Probab=26.42 E-value=59 Score=20.63 Aligned_cols=47 Identities=26% Similarity=0.308 Sum_probs=29.4
Q ss_pred eeEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHH
Q 033831 30 AASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYN 88 (110)
Q Consensus 30 ~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~~~~~p~~al~ 88 (110)
.+.|+|..||.-- |.+. .|+.| --||.+++.++|.|+.-.+-.+|+-
T Consensus 16 kisfeineedyqq-------liel---afsqf--iyplndnieikintkeladnekall 62 (73)
T PHA02766 16 KISFEINEEDYQQ-------LIEL---AFSQF--IYPLNDNIEIKINTKELADNEKALL 62 (73)
T ss_pred EEEEEECHHHHHH-------HHHH---HHHhh--eeeCCCceEEEechHhhccchhhHh
Confidence 4678888888642 2111 12222 3589999999999986545545543
No 70
>PF05465 Halo_GVPC: Halobacterial gas vesicle protein C (GVPC) repeat; InterPro: IPR008639 This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes [,].; GO: 0031412 gas vesicle organization, 0031411 gas vesicle
Probab=26.35 E-value=1.1e+02 Score=16.69 Aligned_cols=21 Identities=33% Similarity=0.512 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 033831 86 AYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 86 al~~a~~~l~~~~~~l~~~f~ 106 (110)
.|..++..+...+......|+
T Consensus 3 ~l~a~I~~~r~~f~~~~~aF~ 23 (32)
T PF05465_consen 3 DLLAAIAEFREEFDDTQDAFE 23 (32)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 455556666666666665554
No 71
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=25.50 E-value=1.5e+02 Score=17.43 Aligned_cols=45 Identities=11% Similarity=0.026 Sum_probs=27.0
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeC
Q 033831 31 ASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTT 78 (110)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~ 78 (110)
+.+.+.++.-.|+-++.-.-..+=+|... |..++ .++..+|++|+
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i-~~~~~--~~~~~~rl~~~ 48 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRAL-SIADT--SEFGILRLIVS 48 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEE-EEEec--CCCCEEEEEEC
Confidence 45566666666666665554555555433 44343 33699999995
No 72
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=25.27 E-value=1.2e+02 Score=21.30 Aligned_cols=53 Identities=23% Similarity=0.378 Sum_probs=36.0
Q ss_pred hHHHHHHHHhcCCCee--eeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 033831 42 IGNILRMQLHRDENVL--FAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEFLD 109 (110)
Q Consensus 42 LgNlLr~~L~~~~~V~--fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~a~ 109 (110)
+.+++|..|++-.=|. ..||- -| ..+|.+.+++-=+.+...++.+++.|+..+
T Consensus 57 v~~l~rrGll~relvqkgWvGYi-------------ya--~~~P~k~leei~~~i~keiEelEk~~k~es 111 (113)
T COG5625 57 VAVLLRRGLLARELVQKGWVGYI-------------YA--TTPPPKPLEEIEEEIMKEIEELEKEFKNES 111 (113)
T ss_pred HHHHHHhhHHHHHHHhccceeeE-------------ec--CCCCchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4566666666532222 45663 22 236788888888899999999999998764
No 73
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=25.01 E-value=50 Score=23.87 Aligned_cols=29 Identities=21% Similarity=0.375 Sum_probs=22.0
Q ss_pred HHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeC
Q 033831 45 ILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTT 78 (110)
Q Consensus 45 lLr~~L~~~~~V~fAgY~vpHPl~~~i~irIqT~ 78 (110)
.+=.+|.++|+|+|||-.-. -.++|+.-.
T Consensus 48 ~~yKqik~np~vefcg~~kd-----g~~vrlrg~ 76 (132)
T COG5015 48 PYYKQIKKNPEVEFCGMDKD-----GVMVRLRGR 76 (132)
T ss_pred HHHHHHhhCCCeEEEEecCC-----ceEEEEeee
Confidence 46678999999999998754 366776543
No 74
>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=24.95 E-value=1.8e+02 Score=25.20 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=23.4
Q ss_pred EEEEec-CCcchHHHHHHHHhcCCCeeeee
Q 033831 32 SFTIER-EEHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 32 ~~~i~~-EDHTLgNlLr~~L~~~~~V~fAg 60 (110)
-+.+.. ...|+.++|+..|.++|+|.+.|
T Consensus 363 q~~v~~~~g~~~~~~l~~~LR~dPDvI~vG 392 (564)
T TIGR02538 363 QVNVNPKIGLTFAAALRSFLRQDPDIIMVG 392 (564)
T ss_pred EEEeccccCCCHHHHHHHHhccCCCEEEeC
Confidence 344443 34799999999999999999988
No 75
>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=24.88 E-value=98 Score=19.39 Aligned_cols=23 Identities=9% Similarity=0.021 Sum_probs=17.1
Q ss_pred eEEEEEeCCCCCHHHHHHHHHHH
Q 033831 71 IIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 71 i~irIqT~~~~~p~~al~~a~~~ 93 (110)
-.-.|+..+|.+..++|..+|+.
T Consensus 11 q~t~V~vrpg~ti~d~L~~~~~k 33 (71)
T PF02196_consen 11 QRTVVQVRPGMTIRDALSKACKK 33 (71)
T ss_dssp EEEEEEE-TTSBHHHHHHHHHHT
T ss_pred CEEEEEEcCCCCHHHHHHHHHHH
Confidence 34456777888999999999864
No 76
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=24.38 E-value=71 Score=26.39 Aligned_cols=37 Identities=14% Similarity=0.091 Sum_probs=29.7
Q ss_pred ceeeEeeccCCCcceeEEEEecCCcchHHHHHHHHhc
Q 033831 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHR 52 (110)
Q Consensus 16 ~~Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~ 52 (110)
...+++...+-..+..+|-+.|-|-.+.|++|..|..
T Consensus 43 ~~~~~V~iv~~~~~~leFDligIda~IANAfRRILia 79 (338)
T KOG1521|consen 43 KDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILIA 79 (338)
T ss_pred hhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHh
Confidence 3444444456677899999999999999999999976
No 77
>PF05986 ADAM_spacer1: ADAM-TS Spacer 1; InterPro: IPR010294 This domain represents the Spacer-1 domain from the ADAM-TS family of metalloproteinases []. A cellular disintegrin and metalloproteinase (ADAM) is a family of genes with structural homology to the snake venom metalloproteinases and disintegrins []. There is variation amongst members of the family, however, all have a similar domain organisation comprising a preproregion, a reprolysin-type catalytic domain, a disintegrin-like domain, a thrombospondin type-1 (TS) module, a cysteine-rich domain, a spacer domain without cysteine residues, and a COOH-terminal TS module [, ]. They are involved in embryogenesis and have been implicated in some cancers and inflammatory diseases [].; GO: 0004222 metalloendopeptidase activity, 0031012 extracellular matrix
Probab=24.23 E-value=2.3e+02 Score=19.09 Aligned_cols=73 Identities=16% Similarity=0.212 Sum_probs=42.9
Q ss_pred CccccceeeCCCceeeEeeccCCCcceeEEEEecCCcchHHHHHHHHhcCCCeeeee----e----------eCCCCCCc
Q 033831 4 PDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG----Y----------KLPHPLQY 69 (110)
Q Consensus 4 p~~~e~~~l~~~~~Kv~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAg----Y----------~vpHPl~~ 69 (110)
+.-.+.+.+|.|...|.+.......|.+-+.-.. ++-+.|-= +.+.....+.+|| | .++.|+..
T Consensus 14 ~gY~~v~~IP~GA~nI~I~e~~~s~n~Lalk~~~-g~y~lNg~-~~i~~~~~~~~aGt~~~Y~~~~~~~E~i~~~GPl~e 91 (114)
T PF05986_consen 14 YGYNKVVTIPAGARNIRITERRPSSNYLALKNSD-GKYVLNGN-WVISWPGTYSVAGTTFEYSRSDDNLERITAPGPLTE 91 (114)
T ss_pred CCceEEEECCCCceEEEEEEeecCccEEEEEecC-CcEEEcCC-ccccCCcCEEeCCeEEEEEecCCCCEEEEcCCCCCC
Confidence 3345788999999999999876666666555333 44444431 1222223355555 2 34567777
Q ss_pred ceEEEEEeC
Q 033831 70 KIIVRIHTT 78 (110)
Q Consensus 70 ~i~irIqT~ 78 (110)
.+.|.|-..
T Consensus 92 ~l~v~vl~~ 100 (114)
T PF05986_consen 92 DLIVQVLSQ 100 (114)
T ss_pred CEEEEEEEe
Confidence 776666443
No 78
>PRK15197 secreted effector protein PipB; Provisional
Probab=24.10 E-value=3.7e+02 Score=21.69 Aligned_cols=42 Identities=5% Similarity=0.086 Sum_probs=27.9
Q ss_pred eeeeeeeC----CCC---CCcceEEEEEeCCCCCHHHHHHHHHHHHHHH
Q 033831 56 VLFAGYKL----PHP---LQYKIIVRIHTTSQSSPMQAYNQAINDLDKE 97 (110)
Q Consensus 56 V~fAgY~v----pHP---l~~~i~irIqT~~~~~p~~al~~a~~~l~~~ 97 (110)
+.|.||.| |-| ..+++.+.|.-.|..-..++..+.+.++-..
T Consensus 84 ~~~~g~~~~fs~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~r~ 132 (291)
T PRK15197 84 EDVNGCTICLSCGAASENTDPMVIIEVNKNGKTVTDKVDSERFWNVCRM 132 (291)
T ss_pred eecCCeEEEeccCCCcccCCceEEEEEecCCcchHHHHHHHHHHHHHHH
Confidence 67889888 333 3566888888666655566666666555554
No 79
>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=23.94 E-value=2e+02 Score=18.17 Aligned_cols=34 Identities=24% Similarity=0.387 Sum_probs=26.2
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 033831 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 72 ~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
.|++...+ .+...||..|++.|...+...++...
T Consensus 60 ~l~a~~~~-~d~~~Aid~a~~klerql~k~k~k~~ 93 (95)
T TIGR00741 60 VIRASAEH-EDMYAAIDLAIDKLERQLRKLKEKRK 93 (95)
T ss_pred EEEEEEec-CcHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 35555443 48999999999999999988877653
No 80
>PHA02781 hypothetical protein; Provisional
Probab=23.69 E-value=68 Score=20.68 Aligned_cols=26 Identities=31% Similarity=0.362 Sum_probs=20.6
Q ss_pred eeeEeeccCCCcceeEEEEecCCcch
Q 033831 17 KKVSYERDTKIINAASFTIEREEHTI 42 (110)
Q Consensus 17 ~Kv~~~~~~~~~n~~~~~i~~EDHTL 42 (110)
-|+++..|++..|-.++...-|.-|+
T Consensus 6 dkikitvdskignvvtisynlekiti 31 (78)
T PHA02781 6 DKIKITVDSKIGNVVTISYNLEKITI 31 (78)
T ss_pred ceEEEEeecccCcEEEEEeeeEEEEE
Confidence 47788888999998888877776664
No 81
>COG0365 Acs Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]
Probab=23.60 E-value=4.9e+02 Score=22.64 Aligned_cols=59 Identities=19% Similarity=0.226 Sum_probs=42.3
Q ss_pred EecCCcchHHH-HHHHHhcCCCeeeeeee-CCCCCCcce-EEEEEeCCCCCHHHHHHHHHHHH
Q 033831 35 IEREEHTIGNI-LRMQLHRDENVLFAGYK-LPHPLQYKI-IVRIHTTSQSSPMQAYNQAINDL 94 (110)
Q Consensus 35 i~~EDHTLgNl-Lr~~L~~~~~V~fAgY~-vpHPl~~~i-~irIqT~~~~~p~~al~~a~~~l 94 (110)
|+--+|.+|.. +-+.|+++|.|.-|+-- +|||....+ ...|.-+.+..|- .|++-+.+.
T Consensus 422 I~vsG~Rig~~EvE~~l~~hP~VaEaAvVg~pd~~kg~~v~afVvL~~g~~~~-~L~~ei~~~ 483 (528)
T COG0365 422 IKVSGKRIGPLEIESVLLAHPAVAEAAVVGVPDPGKGQIVLAFVVLAAGVEPN-ELAEEIRRH 483 (528)
T ss_pred EeccCeeccHHHHHHHHHhCcceeeeEEEeccCCCCCcEEEEEEEecCCCChH-HHHHHHHHH
Confidence 44567888876 67788999999999887 799997664 4455556777776 555555443
No 82
>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=22.90 E-value=1.4e+02 Score=23.21 Aligned_cols=35 Identities=9% Similarity=0.115 Sum_probs=20.7
Q ss_pred eeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033831 58 FAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 58 fAgY~vpHPl~~~i~irIqT~~~~~p~~al~~a~~~l~~~~~ 99 (110)
.++|-+||++... .+.....+.+.+|++++-+.+.
T Consensus 5 v~~~~~~H~~~~~-------~~~~~~~~~~~~al~~~~~~l~ 39 (268)
T cd07367 5 VGAAATSHILMSP-------KGVEDQAARVVQGMAEIGRRVR 39 (268)
T ss_pred EEEEecCCcCcCC-------CCchHHHHHHHHHHHHHHHHHH
Confidence 5789999975442 3333344555666666555543
No 83
>COG2033 Desulfoferrodoxin [Energy production and conversion]
Probab=22.63 E-value=60 Score=23.30 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=8.5
Q ss_pred eeeeCCCCCCcc
Q 033831 59 AGYKLPHPLQYK 70 (110)
Q Consensus 59 AgY~vpHPl~~~ 70 (110)
.| .||||++++
T Consensus 57 VG-~IpHPmt~e 67 (126)
T COG2033 57 VG-EIPHPMTPE 67 (126)
T ss_pred Ec-ccCCCCCCc
Confidence 45 899999755
No 84
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=22.01 E-value=2.7e+02 Score=21.48 Aligned_cols=29 Identities=21% Similarity=0.413 Sum_probs=23.2
Q ss_pred EEEEecC-CcchHHHHHHHHhcCCCeeeee
Q 033831 32 SFTIERE-EHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 32 ~~~i~~E-DHTLgNlLr~~L~~~~~V~fAg 60 (110)
-+.+..+ +-|+..+|+..|..+|+|.+.|
T Consensus 127 q~~v~~~~~~~~~~~l~~~lR~~PD~i~vg 156 (264)
T cd01129 127 QVQVNEKAGLTFARGLRAILRQDPDIIMVG 156 (264)
T ss_pred EEEeCCcCCcCHHHHHHHHhccCCCEEEec
Confidence 3444433 4699999999999999999887
No 85
>PRK15202 type III secretion chaperone protein SigE; Provisional
Probab=21.99 E-value=3e+02 Score=19.48 Aligned_cols=74 Identities=20% Similarity=0.299 Sum_probs=49.1
Q ss_pred CCCceeeEeeccCCCcceeEEEEecCCcchH------------HHHHHHHhcC------------CCeeeeeeeCCCCCC
Q 033831 13 PEGTKKVSYERDTKIINAASFTIEREEHTIG------------NILRMQLHRD------------ENVLFAGYKLPHPLQ 68 (110)
Q Consensus 13 ~~~~~Kv~~~~~~~~~n~~~~~i~~EDHTLg------------NlLr~~L~~~------------~~V~fAgY~vpHPl~ 68 (110)
+++++-+.+- +.+.+-|..++|+|- |-|.+.|.-+ ..+..|-|+.|
T Consensus 17 ~~depaliid------ddi~IYfnes~~~lem~CPf~~LPdn~~~Lq~~LsLNYas~V~la~Dae~t~L~Al~rlp---- 86 (117)
T PRK15202 17 PEDEPALIID------DDIQIYFNESDHTLEMCCPFMPLPDNILTLQHFLSLNYTSAVTLAADAENTALVALYRLP---- 86 (117)
T ss_pred CCCCceEEec------CCeEEEEccCCcchhccCCcccCCccHHHHHHHHhhcccCceEEEEcCCCceEEEeeecC----
Confidence 4555655554 448888899999873 4456666443 23444455555
Q ss_pred cceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033831 69 YKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEF 107 (110)
Q Consensus 69 ~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~f~~ 107 (110)
+++-.+-+.-+.+-.++..+.|++.|.+
T Consensus 87 -----------~~s~~ee~~~g~e~fIs~vr~L~~~~a~ 114 (117)
T PRK15202 87 -----------QTSTEEEALTGFELFISNVKQLKEEYAR 114 (117)
T ss_pred -----------CCCcHHHHHhhHHHHHHHHHHHHHHHhh
Confidence 3455677778888899999999888854
No 86
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=21.80 E-value=1.9e+02 Score=23.90 Aligned_cols=36 Identities=17% Similarity=0.349 Sum_probs=32.4
Q ss_pred cceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033831 69 YKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (110)
Q Consensus 69 ~~i~irIqT~~~~~p~~al~~a~~~l~~~~~~l~~~ 104 (110)
+...+.|.+.|...|...+.+|+.-|...|..++..
T Consensus 301 dHfIFsvestgal~p~~lf~eavkvle~Kc~al~~~ 336 (338)
T KOG1521|consen 301 DHFIFSVESTGALKPEVLFEEAVKVLEEKCRALRDE 336 (338)
T ss_pred ceEEEEeecccCCCchhhHHHHHHHHHHHHHHHhhc
Confidence 448899999999999999999999999999988765
No 87
>KOG0758 consensus Mitochondrial carnitine-acylcarnitine carrier protein [Energy production and conversion]
Probab=21.73 E-value=1.3e+02 Score=24.59 Aligned_cols=33 Identities=18% Similarity=0.411 Sum_probs=23.4
Q ss_pred eeeeCCCCCCcceEEEEEeCCCCC---HHHHHHHHHH
Q 033831 59 AGYKLPHPLQYKIIVRIHTTSQSS---PMQAYNQAIN 92 (110)
Q Consensus 59 AgY~vpHPl~~~i~irIqT~~~~~---p~~al~~a~~ 92 (110)
|+--|-||++ -+.+|+||-.... ..+++++.+.
T Consensus 26 ~~vlVGhPfD-TvKVRlQt~~~~~y~~~~~c~~~t~~ 61 (297)
T KOG0758|consen 26 AQVLVGHPFD-TVKVRLQTQNTPVYKGTLDCVKKTLK 61 (297)
T ss_pred hhhhccCCcc-ceEEeeeccCCCCcccHHHHHHHHHH
Confidence 6667899986 5899999975422 4666666554
No 88
>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=20.30 E-value=64 Score=25.90 Aligned_cols=15 Identities=27% Similarity=0.481 Sum_probs=11.0
Q ss_pred cCCcchHHHHHHHHh
Q 033831 37 REEHTIGNILRMQLH 51 (110)
Q Consensus 37 ~EDHTLgNlLr~~L~ 51 (110)
-.+|+|||+++..++
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 468999999996654
Done!