Query 033845
Match_columns 110
No_of_seqs 104 out of 468
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 06:57:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033845.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033845hhsearch_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 7.4E-45 1.6E-49 252.4 12.3 110 1-110 1-110 (117)
2 cd06926 RNAP_II_RPB11 RPB11 su 100.0 2.7E-39 5.7E-44 219.0 11.8 93 13-105 1-93 (93)
3 PF13656 RNA_pol_L_2: RNA poly 100.0 1.8E-36 3.8E-41 198.9 8.7 77 29-105 1-77 (77)
4 cd07029 RNAP_I_III_AC19 AC19 s 100.0 3.6E-36 7.9E-41 200.8 10.2 82 24-105 4-85 (85)
5 PRK01146 DNA-directed RNA poly 100.0 2.2E-35 4.7E-40 197.1 10.7 80 24-103 6-85 (85)
6 cd06927 RNAP_L L subunit of Ar 100.0 5E-35 1.1E-39 194.6 10.1 78 25-102 5-82 (83)
7 cd07027 RNAP_RPB11_like RPB11 100.0 9.7E-35 2.1E-39 193.2 10.3 78 25-102 5-82 (83)
8 COG1761 RPB11 DNA-directed RNA 100.0 8.9E-34 1.9E-38 194.2 12.4 93 16-109 2-94 (99)
9 KOG3438 DNA-directed RNA polym 100.0 7.5E-32 1.6E-36 184.6 9.6 84 26-109 13-96 (105)
10 cd00460 RNAP_RPB11_RPB3 RPB11 99.9 1.7E-26 3.7E-31 153.7 9.7 76 25-101 5-86 (86)
11 PF01193 RNA_pol_L: RNA polyme 99.7 1.6E-17 3.4E-22 105.3 4.8 65 31-99 1-66 (66)
12 PRK14979 DNA-directed RNA poly 96.0 0.037 8E-07 42.1 7.1 51 53-107 138-188 (195)
13 cd06928 RNAP_alpha_NTD N-termi 95.7 0.024 5.2E-07 43.2 5.0 45 55-99 163-213 (215)
14 cd07028 RNAP_RPB3_like RPB3 su 95.6 0.039 8.5E-07 42.2 6.0 52 51-103 160-211 (212)
15 smart00662 RPOLD RNA polymeras 95.3 0.039 8.5E-07 42.2 5.2 46 55-100 162-223 (224)
16 TIGR02027 rpoA DNA-directed RN 95.3 0.06 1.3E-06 43.1 6.3 49 55-103 154-208 (297)
17 PRK00783 DNA-directed RNA poly 95.1 0.029 6.4E-07 43.5 3.9 36 18-55 2-38 (263)
18 PRK05182 DNA-directed RNA poly 94.7 0.1 2.2E-06 42.0 6.0 50 54-103 170-225 (310)
19 CHL00013 rpoA RNA polymerase a 94.6 0.094 2E-06 42.7 5.8 50 54-103 169-223 (327)
20 cd07030 RNAP_D D subunit of Ar 94.3 0.061 1.3E-06 41.7 4.0 36 18-55 2-38 (259)
21 CHL00013 rpoA RNA polymerase a 94.1 0.12 2.5E-06 42.2 5.3 48 18-65 9-61 (327)
22 PRK05182 DNA-directed RNA poly 94.1 0.13 2.8E-06 41.5 5.5 47 18-64 8-59 (310)
23 cd06928 RNAP_alpha_NTD N-termi 93.4 0.14 3E-06 39.1 4.4 40 25-64 5-49 (215)
24 cd07028 RNAP_RPB3_like RPB3 su 93.3 0.11 2.3E-06 39.8 3.5 32 25-56 7-39 (212)
25 cd07031 RNAP_II_RPB3 RPB3 subu 93.2 0.28 6.1E-06 38.6 5.9 40 68-107 225-264 (265)
26 PRK14979 DNA-directed RNA poly 92.0 0.21 4.5E-06 38.0 3.6 39 21-60 6-45 (195)
27 cd07031 RNAP_II_RPB3 RPB3 subu 91.9 0.43 9.3E-06 37.6 5.4 38 18-57 2-40 (265)
28 COG0202 RpoA DNA-directed RNA 90.9 0.54 1.2E-05 38.1 5.2 45 19-63 7-54 (317)
29 smart00662 RPOLD RNA polymeras 90.6 0.38 8.3E-06 36.8 3.9 33 31-63 2-35 (224)
30 PRK00783 DNA-directed RNA poly 90.4 0.84 1.8E-05 35.4 5.7 41 67-107 221-261 (263)
31 cd07030 RNAP_D D subunit of Ar 88.0 1.3 2.8E-05 34.3 5.2 37 68-104 222-258 (259)
32 cd07032 RNAP_I_II_AC40 AC40 su 85.4 2.3 5E-05 34.2 5.4 37 67-103 254-290 (291)
33 TIGR02027 rpoA DNA-directed RN 84.7 1.3 2.7E-05 35.5 3.6 29 36-64 11-40 (297)
34 COG2805 PilT Tfp pilus assembl 68.8 3.1 6.8E-05 34.3 1.7 24 38-61 183-206 (353)
35 cd04905 ACT_CM-PDT C-terminal 67.8 27 0.00058 21.7 6.6 68 30-99 3-71 (80)
36 cd02071 MM_CoA_mut_B12_BD meth 66.6 18 0.0004 24.5 5.0 27 31-57 3-29 (122)
37 cd02067 B12-binding B12 bindin 57.1 30 0.00064 23.0 4.6 27 31-57 3-29 (119)
38 COG0202 RpoA DNA-directed RNA 55.8 20 0.00044 29.1 4.2 38 69-106 188-225 (317)
39 cd07032 RNAP_I_II_AC40 AC40 su 53.5 22 0.00049 28.5 4.0 34 18-53 2-35 (291)
40 PRK02261 methylaspartate mutas 52.8 48 0.001 23.3 5.3 37 28-64 4-42 (137)
41 PF05986 ADAM_spacer1: ADAM-TS 49.6 69 0.0015 21.7 5.5 73 4-78 14-100 (114)
42 KOG1522 RNA polymerase II, sub 48.2 44 0.00096 26.8 4.9 75 29-106 175-266 (285)
43 cd02070 corrinoid_protein_B12- 46.2 41 0.0009 24.8 4.3 68 29-96 84-159 (201)
44 PF06657 Cep57_MT_bd: Centroso 45.0 67 0.0015 20.8 4.6 28 79-106 7-34 (79)
45 TIGR02370 pyl_corrinoid methyl 43.9 52 0.0011 24.4 4.5 38 28-65 85-124 (197)
46 cd02069 methionine_synthase_B1 41.3 56 0.0012 24.7 4.4 69 28-96 89-165 (213)
47 PRK00549 competence damage-ind 40.5 1.3E+02 0.0028 25.1 6.8 62 32-99 182-244 (414)
48 PF03633 Glyco_hydro_65C: Glyc 38.8 26 0.00057 20.4 1.8 25 17-42 28-52 (54)
49 KOG2972 Uncharacterized conser 38.1 91 0.002 25.1 5.2 40 41-80 93-133 (276)
50 PRK12729 fliE flagellar hook-b 36.4 1.2E+02 0.0027 21.7 5.2 16 82-97 57-72 (127)
51 KOG0758 Mitochondrial carnitin 36.1 51 0.0011 26.8 3.6 33 58-91 25-60 (297)
52 COG2804 PulE Type II secretory 35.6 32 0.00069 29.9 2.5 25 36-60 310-334 (500)
53 KOG0762 Mitochondrial carrier 35.3 31 0.00067 27.8 2.2 26 58-84 24-49 (311)
54 COG1544 Ribosome-associated pr 35.0 1.5E+02 0.0033 20.4 6.2 28 81-108 70-97 (110)
55 PRK01215 competence damage-ind 34.3 2.3E+02 0.0049 22.2 7.4 68 32-104 183-255 (264)
56 PRK10470 ribosome hibernation 34.1 1.3E+02 0.0028 19.3 5.1 34 72-106 60-93 (95)
57 PF00437 T2SE: Type II/IV secr 33.7 1.2E+02 0.0027 22.8 5.3 34 27-60 171-204 (270)
58 TIGR00741 yfiA ribosomal subun 33.4 1.3E+02 0.0028 19.1 5.1 34 72-106 60-93 (95)
59 PF11470 TUG-UBL1: GLUT4 regul 31.4 73 0.0016 19.9 3.1 24 71-94 7-30 (65)
60 PHA02781 hypothetical protein; 30.5 45 0.00096 21.5 1.9 26 17-42 6-31 (78)
61 PF02482 Ribosomal_S30AE: Sigm 30.2 1.5E+02 0.0031 18.7 4.7 33 72-105 62-94 (97)
62 TIGR01546 GAPDH-II_archae glyc 28.5 1.5E+02 0.0033 24.2 5.2 50 40-92 190-239 (333)
63 COG3062 NapD Uncharacterized p 28.3 2E+02 0.0043 19.6 5.2 44 43-94 20-63 (94)
64 PF00403 HMA: Heavy-metal-asso 28.2 1.3E+02 0.0027 17.4 5.9 47 42-93 12-58 (62)
65 PRK15202 type III secretion ch 28.1 2.2E+02 0.0047 20.1 9.3 75 12-107 16-114 (117)
66 COG4245 TerY Uncharacterized p 27.9 1E+02 0.0022 23.9 3.8 38 71-108 6-45 (207)
67 cd00552 RaiA RaiA ("ribosome-a 27.7 1.4E+02 0.003 18.7 4.0 22 81-102 70-91 (93)
68 PLN02231 alanine transaminase 27.6 2.8E+02 0.006 23.8 6.9 58 46-106 476-533 (534)
69 COG5625 Predicted transcriptio 27.5 1E+02 0.0023 21.5 3.5 27 82-108 84-110 (113)
70 PRK04207 glyceraldehyde-3-phos 26.9 2.6E+02 0.0056 22.5 6.3 51 40-93 193-243 (341)
71 PHA02766 hypothetical protein; 26.9 58 0.0013 20.6 2.0 50 30-91 16-65 (73)
72 KOG0359 Chaperonin complex com 26.5 75 0.0016 27.6 3.2 38 15-52 348-389 (520)
73 PF05465 Halo_GVPC: Halobacter 26.5 1.2E+02 0.0026 16.5 3.0 21 86-106 3-23 (32)
74 TIGR02538 type_IV_pilB type IV 25.9 1.7E+02 0.0037 25.3 5.3 30 31-60 362-392 (564)
75 cd01760 RBD Ubiquitin-like dom 25.6 1.1E+02 0.0025 19.4 3.3 21 73-93 12-32 (72)
76 COG5015 Uncharacterized conser 24.6 51 0.0011 23.8 1.6 28 45-77 48-75 (132)
77 cd01129 PulE-GspE PulE/GspE Th 24.3 2.3E+02 0.005 21.8 5.4 32 29-60 124-156 (264)
78 COG2033 Desulfoferrodoxin [Ene 23.4 57 0.0012 23.4 1.6 11 59-70 57-67 (126)
79 COG1058 CinA Predicted nucleot 23.1 2.8E+02 0.0062 21.9 5.7 69 31-102 181-250 (255)
80 PRK15197 secreted effector pro 23.0 4E+02 0.0087 21.4 6.6 42 56-97 84-132 (291)
81 PF14185 SpoIISB_antitox: Anti 22.8 15 0.00033 22.7 -1.2 15 51-65 21-36 (56)
82 PF02196 RBD: Raf-like Ras-bin 22.8 1.1E+02 0.0025 19.1 2.8 23 71-93 11-33 (71)
83 TIGR00444 mazG MazG family pro 22.4 1.8E+02 0.0039 22.8 4.4 27 80-106 200-226 (248)
84 smart00455 RBD Raf-like Ras-bi 22.2 2.1E+02 0.0045 17.8 4.0 23 71-93 10-32 (70)
85 COG2921 Uncharacterized conser 21.5 2.7E+02 0.0059 18.8 4.8 47 12-58 41-88 (90)
86 KOG1521 RNA polymerase I and I 21.5 1.8E+02 0.0038 24.1 4.3 54 44-104 283-336 (338)
87 KOG1522 RNA polymerase II, sub 21.0 1.3E+02 0.0029 24.2 3.4 37 17-55 6-43 (285)
88 PTZ00377 alanine aminotransfer 21.0 4.5E+02 0.0098 21.7 6.8 57 46-105 424-480 (481)
89 cd04908 ACT_Bt0572_1 N-termina 20.9 1.9E+02 0.0042 16.9 5.2 45 31-78 4-48 (66)
90 PLN02150 terpene synthase/cycl 20.8 1.6E+02 0.0035 19.5 3.4 23 88-110 22-44 (96)
91 cd07353 harmonin_N N-terminal 20.7 36 0.00079 22.3 0.2 16 1-19 49-64 (79)
92 cd04402 RhoGAP_ARHGAP20 RhoGAP 20.4 20 0.00043 26.4 -1.2 51 4-55 31-82 (192)
93 PF14318 Mononeg_mRNAcap: Mono 20.2 56 0.0012 25.3 1.2 25 41-68 5-29 (245)
94 cd07367 CarBb CarBb is the B s 20.2 1.6E+02 0.0036 22.8 3.8 35 58-99 5-39 (268)
95 PF09137 Glucodextran_N: Gluco 20.2 92 0.002 24.8 2.4 38 70-109 225-262 (269)
96 PHA02729 hypothetical protein; 20.0 1.4E+02 0.0031 20.2 2.9 59 3-61 7-67 (94)
No 1
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=7.4e-45 Score=252.44 Aligned_cols=110 Identities=52% Similarity=0.839 Sum_probs=108.8
Q ss_pred CCCCccccceecCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033845 1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ 80 (110)
Q Consensus 1 mn~p~~~~~~~l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~ 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 CCHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q 033845 81 SSPMQAYNQAINDLDKELDTLKSAFEVKHL 110 (110)
Q Consensus 81 ~~P~~al~~a~~~l~~~~~~l~~~f~~~~~ 110 (110)
++|.++|.+|+.++...++.++.+|+.+|.
T Consensus 81 ~~p~~al~~a~~~l~~el~~l~~~f~~~~~ 110 (117)
T KOG4392|consen 81 CSPADALTNAITDLIEELSLLENRFKAEAA 110 (117)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999983
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=2.7e-39 Score=219.02 Aligned_cols=93 Identities=57% Similarity=0.903 Sum_probs=91.1
Q ss_pred CCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHH
Q 033845 13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92 (110)
Q Consensus 13 ~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 033845 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 9999999999876
No 3
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=100.00 E-value=1.8e-36 Score=198.86 Aligned_cols=77 Identities=47% Similarity=0.788 Sum_probs=72.8
Q ss_pred ceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 29 n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 78999999999999999999999999999999999999999999999999999999999999999999999999987
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=3.6e-36 Score=200.83 Aligned_cols=82 Identities=32% Similarity=0.575 Sum_probs=79.5
Q ss_pred cCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 24 ~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 033845 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 76
No 5
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=100.00 E-value=2.2e-35 Score=197.09 Aligned_cols=80 Identities=29% Similarity=0.392 Sum_probs=77.0
Q ss_pred cCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 24 ~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~ 103 (110)
.++.+|+++|+|.||||||||+||++|+++|+|.||||++|||++++++|||||+++.+|.+||++|+++|++.|++|++
T Consensus 6 i~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~~ 85 (85)
T PRK01146 6 LEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD 85 (85)
T ss_pred EecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999863
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=5e-35 Score=194.60 Aligned_cols=78 Identities=31% Similarity=0.446 Sum_probs=75.9
Q ss_pred CCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033845 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102 (110)
Q Consensus 25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 468999999999999999999999999999999999999999999999999999989999999999999999999986
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=9.7e-35 Score=193.20 Aligned_cols=78 Identities=40% Similarity=0.614 Sum_probs=75.5
Q ss_pred CCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033845 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102 (110)
Q Consensus 25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 467899999999999999999999999999999999999999999999999999989999999999999999999885
No 8
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=8.9e-34 Score=194.16 Aligned_cols=93 Identities=35% Similarity=0.532 Sum_probs=88.6
Q ss_pred ceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHH
Q 033845 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD 95 (110)
Q Consensus 16 ~~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 46677777789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhh
Q 033845 96 KELDTLKSAFEVKH 109 (110)
Q Consensus 96 ~~~~~l~~~f~~~~ 109 (110)
+.|++|..+| ++|
T Consensus 82 ~~~~~l~~~~-~~~ 94 (99)
T COG1761 82 KDLEELLDQF-EEF 94 (99)
T ss_pred HHHHHHHHHH-HHH
Confidence 9999999988 776
No 9
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=99.97 E-value=7.5e-32 Score=184.61 Aligned_cols=84 Identities=31% Similarity=0.594 Sum_probs=80.9
Q ss_pred CCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 26 k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 37799999999999999999999999999999999999999999999999999888899999999999999999999999
Q ss_pred Hhhh
Q 033845 106 EVKH 109 (110)
Q Consensus 106 ~~~~ 109 (110)
++++
T Consensus 93 ~~~i 96 (105)
T KOG3438|consen 93 EEEI 96 (105)
T ss_pred HHHH
Confidence 9875
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=1.7e-26 Score=153.68 Aligned_cols=76 Identities=39% Similarity=0.592 Sum_probs=72.8
Q ss_pred CCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCC------CcceEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q 033845 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDKEL 98 (110)
Q Consensus 25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl------~~~~~lrIqT~~~~~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 033845 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=99.70 E-value=1.6e-17 Score=105.25 Aligned_cols=65 Identities=35% Similarity=0.556 Sum_probs=61.1
Q ss_pred eEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 31 ~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 99999999999999999999999999999998773
No 12
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=95.97 E-value=0.037 Score=42.06 Aligned_cols=51 Identities=14% Similarity=0.147 Sum_probs=42.3
Q ss_pred CCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845 53 DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107 (110)
Q Consensus 53 ~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 5564322 4899999999999999999999999999999999988764
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=95.67 E-value=0.024 Score=43.25 Aligned_cols=45 Identities=27% Similarity=0.240 Sum_probs=37.3
Q ss_pred CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845 55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 55 ~V~fAgY~vpH------Pl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~ 99 (110)
=|.-+.|.|.- .-.+++.|-|.|+|+++|.+||..|++.|.+.+.
T Consensus 163 PV~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~ 213 (215)
T cd06928 163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFS 213 (215)
T ss_pred CeEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhh
Confidence 36677888643 3357899999999999999999999999988775
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=95.62 E-value=0.039 Score=42.20 Aligned_cols=52 Identities=17% Similarity=0.262 Sum_probs=43.9
Q ss_pred hcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 51 HRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 51 ~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 34455677889864 36689999999999999999999999999999998875
No 15
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=95.35 E-value=0.039 Score=42.21 Aligned_cols=46 Identities=24% Similarity=0.299 Sum_probs=38.0
Q ss_pred CeeeeeeeCCCCC----------------CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033845 55 NVLFAGYKLPHPL----------------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT 100 (110)
Q Consensus 55 ~V~fAgY~vpHPl----------------~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~ 100 (110)
.|..+.|.+.-|- .+++.|.|.|+|..+|.+||.+|++-|...++.
T Consensus 162 pv~~v~~~~~~~~~~~~~~~~~~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~ 223 (224)
T smart00662 162 PVDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 223 (224)
T ss_pred hhhheeeeccCCccceecccchhhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence 3555667776664 478999999999999999999999999888764
No 16
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=95.29 E-value=0.06 Score=43.06 Aligned_cols=49 Identities=24% Similarity=0.310 Sum_probs=40.4
Q ss_pred CeeeeeeeCCC------CCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 55 ~V~fAgY~vpH------Pl~~~~~lrIqT~~~~~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 35667787653 22468999999999999999999999999999988854
No 17
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=95.09 E-value=0.029 Score=43.54 Aligned_cols=36 Identities=17% Similarity=0.172 Sum_probs=29.5
Q ss_pred eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CC
Q 033845 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN 55 (110)
Q Consensus 18 Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~ 55 (110)
++++.+. .++.++|.+.|-++|+||+||-.|+.. |.
T Consensus 2 ~~~~~~~--~~~~~~f~~~g~~~t~~NalRRvlls~vp~ 38 (263)
T PRK00783 2 EIEILEL--DDRSARFVVEGVTPAFANAIRRAMIADVPT 38 (263)
T ss_pred ceEEEEc--CCcEEEEEEeCCCHHHHHHHHHHHHHcCCe
Confidence 4566654 558899999999999999999999985 44
No 18
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=94.65 E-value=0.1 Score=42.02 Aligned_cols=50 Identities=20% Similarity=0.228 Sum_probs=40.8
Q ss_pred CCeeeeeeeCCCC------CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 54 ENVLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 54 ~~V~fAgY~vpHP------l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~ 103 (110)
.-|.-+.|.+.-. -.+++.|.|.|+|+++|.+||.+|++.|...+..|.+
T Consensus 170 ~PV~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~ 225 (310)
T PRK05182 170 SPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD 225 (310)
T ss_pred CCccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 3366678876542 1468999999999999999999999999999887754
No 19
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=94.61 E-value=0.094 Score=42.67 Aligned_cols=50 Identities=18% Similarity=0.152 Sum_probs=41.2
Q ss_pred CCeeeeeeeCCCC-----CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 54 ENVLFAGYKLPHP-----LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 54 ~~V~fAgY~vpHP-----l~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~ 103 (110)
.=|.-+.|.|..- ..+++.|-|.|+|+++|.+||..|++.|.+.+.-|.+
T Consensus 169 sPV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~ 223 (327)
T CHL00013 169 MPVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH 223 (327)
T ss_pred CCeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 3466777887651 2578999999999999999999999999999887753
No 20
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=94.33 E-value=0.061 Score=41.69 Aligned_cols=36 Identities=14% Similarity=0.167 Sum_probs=29.7
Q ss_pred eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CC
Q 033845 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN 55 (110)
Q Consensus 18 Ki~~~~~~k~~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 456665 3568999999999999999999999985 44
No 21
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=94.11 E-value=0.12 Score=42.16 Aligned_cols=48 Identities=25% Similarity=0.237 Sum_probs=38.6
Q ss_pred eeEeeecCCCcceeEEEE----ccCCcchHHHHHHHHhc-CCCeeeeeeeCCC
Q 033845 18 KVSYERDTKIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH 65 (110)
Q Consensus 18 Ki~~~~~~k~~n~~~~~i----~~EDHTlgNlLr~~L~~-~~~V~fAgY~vpH 65 (110)
-++........+.+.|.| .|..|||||+||-.|++ .|+.-+.+-++.+
T Consensus 9 ~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 9 CVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred ceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 355666677889999999 67889999999999998 4877777767654
No 22
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=94.10 E-value=0.13 Score=41.46 Aligned_cols=47 Identities=26% Similarity=0.311 Sum_probs=35.8
Q ss_pred eeEeeecCCCcceeEEEEc----cCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q 033845 18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKLP 64 (110)
Q Consensus 18 Ki~~~~~~k~~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 4555544335799999996 99999999999999984 76666665554
No 23
>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=93.44 E-value=0.14 Score=39.12 Aligned_cols=40 Identities=28% Similarity=0.331 Sum_probs=31.6
Q ss_pred CCCcceeEEEE----ccCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q 033845 25 TKIINAASFTI----EREEHTIGNILRMQLHRD-ENVLFAGYKLP 64 (110)
Q Consensus 25 ~k~~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 44578999999 789999999999999984 66655555543
No 24
>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=93.25 E-value=0.11 Score=39.84 Aligned_cols=32 Identities=13% Similarity=0.208 Sum_probs=28.0
Q ss_pred CCCcceeEEEEccCCcchHHHHHHHHhcC-CCe
Q 033845 25 TKIINAASFTIEREEHTIGNILRMQLHRD-ENV 56 (110)
Q Consensus 25 ~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V 56 (110)
.+.++.++|.+.|-|+|+||+||-.|+.. |..
T Consensus 7 ~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~ 39 (212)
T cd07028 7 EADKDNVDFILSGVDLAMANALRRVMIAEVPTM 39 (212)
T ss_pred EcCCCEEEEEEEccChhHHHHHHHHHHHcCcce
Confidence 46889999999999999999999999985 543
No 25
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=93.19 E-value=0.28 Score=38.59 Aligned_cols=40 Identities=20% Similarity=0.227 Sum_probs=37.0
Q ss_pred CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107 (110)
Q Consensus 68 ~~~~~lrIqT~~~~~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 5779999999999999999999999999999999998764
No 26
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=92.00 E-value=0.21 Score=37.97 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=31.2
Q ss_pred eeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CCeeeee
Q 033845 21 YERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAG 60 (110)
Q Consensus 21 ~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAg 60 (110)
+..-+|..+.++|.+. -+.|+||+||-.|+.. |+.-.-+
T Consensus 6 ~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~ 45 (195)
T PRK14979 6 EKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN 45 (195)
T ss_pred eeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence 3344788999999999 9999999999999984 6544444
No 27
>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=91.93 E-value=0.43 Score=37.57 Aligned_cols=38 Identities=16% Similarity=0.274 Sum_probs=30.5
Q ss_pred eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC-CCee
Q 033845 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVL 57 (110)
Q Consensus 18 Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~ 57 (110)
+|++.+ ..++.++|.+.+=|+|+||+||-.|+.. |..-
T Consensus 2 ~i~i~~--~~~~~~~F~l~~~~~s~aNALRRillsevPt~A 40 (265)
T cd07031 2 RVEITE--LTDDKVKFILENTDLSVANSLRRVMIAEVPTLA 40 (265)
T ss_pred cEEEEE--cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccce
Confidence 456665 4568999999999999999999999984 5433
No 28
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=90.94 E-value=0.54 Score=38.10 Aligned_cols=45 Identities=18% Similarity=0.049 Sum_probs=32.7
Q ss_pred eEeeecC--CCcceeEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeC
Q 033845 19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL 63 (110)
Q Consensus 19 i~~~~~~--k~~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 4555443 3477889999999999999999999984 6644444333
No 29
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=90.60 E-value=0.38 Score=36.76 Aligned_cols=33 Identities=24% Similarity=0.299 Sum_probs=26.3
Q ss_pred eEEEEccCCcchHHHHHHHHhcC-CCeeeeeeeC
Q 033845 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL 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 67999999999999999999984 6655544444
No 30
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=90.39 E-value=0.84 Score=35.39 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=37.3
Q ss_pred CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845 67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107 (110)
Q Consensus 67 l~~~~~lrIqT~~~~~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 35678899999999999999999999999999999998865
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=88.04 E-value=1.3 Score=34.26 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=33.3
Q ss_pred CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033845 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (110)
Q Consensus 68 ~~~~~lrIqT~~~~~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 4557888999999999999999999999999999875
No 32
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=85.41 E-value=2.3 Score=34.17 Aligned_cols=37 Identities=22% Similarity=0.266 Sum_probs=33.6
Q ss_pred CCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033845 67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (110)
Q Consensus 67 l~~~~~lrIqT~~~~~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 3566999999999999999999999999999999875
No 33
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=84.69 E-value=1.3 Score=35.54 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=23.4
Q ss_pred ccCCcchHHHHHHHHhcC-CCeeeeeeeCC
Q 033845 36 EREEHTIGNILRMQLHRD-ENVLFAGYKLP 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 588999999999999984 77766666554
No 34
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=68.81 E-value=3.1 Score=34.35 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=21.8
Q ss_pred CCcchHHHHHHHHhcCCCeeeeee
Q 033845 38 EEHTIGNILRMQLHRDENVLFAGY 61 (110)
Q Consensus 38 EDHTlgNlLr~~L~~~~~V~fAgY 61 (110)
-.|++.|.||..|.+||+|.+.|=
T Consensus 183 dT~sF~~aLraALReDPDVIlvGE 206 (353)
T COG2805 183 DTLSFANALRAALREDPDVILVGE 206 (353)
T ss_pred cHHHHHHHHHHHhhcCCCEEEEec
Confidence 459999999999999999999993
No 35
>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=67.82 E-value=27 Score=21.70 Aligned_cols=68 Identities=13% Similarity=0.164 Sum_probs=38.5
Q ss_pred eeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCC-CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845 30 AASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL-QYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 30 ~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl-~~~~~lrIqT~~~~~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 455666555445555554443333333222 2334432 456889999987533 4778888888776554
No 36
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=66.62 E-value=18 Score=24.55 Aligned_cols=27 Identities=15% Similarity=0.051 Sum_probs=22.8
Q ss_pred eEEEEccCCcchHHHHHHHHhcCCCee
Q 033845 31 ASFTIEREEHTIGNILRMQLHRDENVL 57 (110)
Q Consensus 31 ~~~~i~~EDHTlgNlLr~~L~~~~~V~ 57 (110)
+..++.+|.|++|..+...+++..+.+
T Consensus 3 v~~~~~gd~H~lG~~~~~~~l~~~G~~ 29 (122)
T cd02071 3 LVAKPGLDGHDRGAKVIARALRDAGFE 29 (122)
T ss_pred EEEecCCChhHHHHHHHHHHHHHCCCE
Confidence 567889999999999999999986533
No 37
>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=57.08 E-value=30 Score=22.96 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=22.1
Q ss_pred eEEEEccCCcchHHHHHHHHhcCCCee
Q 033845 31 ASFTIEREEHTIGNILRMQLHRDENVL 57 (110)
Q Consensus 31 ~~~~i~~EDHTlgNlLr~~L~~~~~V~ 57 (110)
+-.+..+|.|++|..+-..+++..+.+
T Consensus 3 l~~~~~~e~H~lG~~~~~~~l~~~G~~ 29 (119)
T cd02067 3 VIATVGGDGHDIGKNIVARALRDAGFE 29 (119)
T ss_pred EEEeeCCchhhHHHHHHHHHHHHCCCE
Confidence 456789999999999999999876543
No 38
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=55.80 E-value=20 Score=29.05 Aligned_cols=38 Identities=16% Similarity=0.075 Sum_probs=33.6
Q ss_pred cceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 69 YKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 69 ~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
++..+.+-|++++.|.+|+..|.+-+.+.|+.+.+.+.
T Consensus 188 Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~ 225 (317)
T COG0202 188 DHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCP 225 (317)
T ss_pred eeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhcc
Confidence 56778888999999999999999999999999887764
No 39
>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=53.51 E-value=22 Score=28.54 Aligned_cols=34 Identities=18% Similarity=0.174 Sum_probs=28.7
Q ss_pred eeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcC
Q 033845 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (110)
Q Consensus 18 Ki~~~~~~k~~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 455654 5678999999999999999999998874
No 40
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=52.82 E-value=48 Score=23.32 Aligned_cols=37 Identities=16% Similarity=0.143 Sum_probs=28.0
Q ss_pred cceeEEEEccCCcchHHHHHHHHhcCCC--eeeeeeeCC
Q 033845 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 3457788899999999999999999754 444454444
No 41
>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=49.63 E-value=69 Score=21.72 Aligned_cols=73 Identities=16% Similarity=0.212 Sum_probs=45.3
Q ss_pred CccccceecCCCceeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhcCCCeeeee----e----------eCCCCCCc
Q 033845 4 PDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG----Y----------KLPHPLQY 69 (110)
Q Consensus 4 p~~~~~~~l~~~~~Ki~~~~~~k~~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 3445789999999999999887666776655444 55555442 2233334456665 2 34567766
Q ss_pred ceEEEEEeC
Q 033845 70 KIIVRIHTT 78 (110)
Q Consensus 70 ~~~lrIqT~ 78 (110)
.+.|.|-..
T Consensus 92 ~l~v~vl~~ 100 (114)
T PF05986_consen 92 DLIVQVLSQ 100 (114)
T ss_pred CEEEEEEEe
Confidence 666655443
No 42
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=48.24 E-value=44 Score=26.81 Aligned_cols=75 Identities=19% Similarity=0.165 Sum_probs=54.2
Q ss_pred ceeEEEEccCCcchHHHHHHHHh--------cCCCeeeeeeeCCCC----C-----CcceEEEEEeCCCCCHHHHHHHHH
Q 033845 29 NAASFTIEREEHTIGNILRMQLH--------RDENVLFAGYKLPHP----L-----QYKIIVRIHTTSQSSPMQAYNQAI 91 (110)
Q Consensus 29 n~~~~~i~~EDHTlgNlLr~~L~--------~~~~V~fAgY~vpHP----l-----~~~~~lrIqT~~~~~P~~al~~a~ 91 (110)
-++.+.|.-+-- |.||+.+. +-|+++.+++.-+-| . -+++++.|.+.|+..|.+++..|+
T Consensus 175 Pta~V~FeYDPd---n~lrhT~y~~e~~~~~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi 251 (285)
T KOG1522|consen 175 PTAAVAFEYDPD---NKLRHTLYWFEEDDLIEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGI 251 (285)
T ss_pred CcceEEEEECcc---HhhhccCCCccccchhhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHH
Confidence 344555533222 77777664 446778888776511 1 277999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 033845 92 NDLDKELDTLKSAFE 106 (110)
Q Consensus 92 ~~l~~~~~~l~~~f~ 106 (110)
+-|.+.++.+..+..
T Consensus 252 ~iLk~Kl~~l~~~l~ 266 (285)
T KOG1522|consen 252 DILKEKLAALRLALS 266 (285)
T ss_pred HHHHHHHHHHHhhhc
Confidence 999999998877654
No 43
>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=46.16 E-value=41 Score=24.78 Aligned_cols=68 Identities=19% Similarity=0.201 Sum_probs=40.1
Q ss_pred ceeEEEEccCCcchHHHHHHHHhcCCC--eeeeeeeCCCCC------CcceEEEEEeCCCCCHHHHHHHHHHHHHH
Q 033845 29 NAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDK 96 (110)
Q Consensus 29 n~~~~~i~~EDHTlgNlLr~~L~~~~~--V~fAgY~vpHPl------~~~~~lrIqT~~~~~P~~al~~a~~~l~~ 96 (110)
..+..++.||.|+||-.+...+++..+ |.+.|-.+|+.- +..+.+..-+-........+++.++.|.+
T Consensus 84 ~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~~~d~v~lS~~~~~~~~~~~~~i~~lr~ 159 (201)
T cd02070 84 KVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEALKE 159 (201)
T ss_pred eEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHH
Confidence 446678899999999988888888754 445566666542 23333322222111234555555555544
No 44
>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=45.00 E-value=67 Score=20.79 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 79 SQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 79 ~~~~P~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
++.+|.++|...+..|.+++.++.-.+.
T Consensus 7 ~s~~p~~~Ls~vl~~LqDE~~hm~~e~~ 34 (79)
T PF06657_consen 7 PSQSPGEALSEVLKALQDEFGHMKMEHQ 34 (79)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999999987664
No 45
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=43.93 E-value=52 Score=24.36 Aligned_cols=38 Identities=21% Similarity=0.270 Sum_probs=29.5
Q ss_pred cceeEEEEccCCcchHHHHHHHHhcCCC--eeeeeeeCCC
Q 033845 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPH 65 (110)
Q Consensus 28 ~n~~~~~i~~EDHTlgNlLr~~L~~~~~--V~fAgY~vpH 65 (110)
..-+-.++.||.|.+|-.+...+++..+ |.+.|-.+|-
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~ 124 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPI 124 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCH
Confidence 3457778899999999999999999754 5566666664
No 46
>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=41.34 E-value=56 Score=24.69 Aligned_cols=69 Identities=13% Similarity=0.124 Sum_probs=41.0
Q ss_pred cceeEEEEccCCcchHHHHHHHHhcCCC--eeeeeeeCCCCC------CcceEEEEEeCCCCCHHHHHHHHHHHHHH
Q 033845 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDK 96 (110)
Q Consensus 28 ~n~~~~~i~~EDHTlgNlLr~~L~~~~~--V~fAgY~vpHPl------~~~~~lrIqT~~~~~P~~al~~a~~~l~~ 96 (110)
...+-.++.||.|.||-.+...+++..+ |.+-|-++|-+- +.++.+..-+-...+....+++.++.|.+
T Consensus 89 ~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~~~~~V~lS~~~~~~~~~~~~~i~~L~~ 165 (213)
T cd02069 89 GKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIEKILEAAKEHKADIIGLSGLLVPSLDEMVEVAEEMNR 165 (213)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEccchhccHHHHHHHHHHHHh
Confidence 3456778899999999999999999754 556666665332 23333332222112334555555555543
No 47
>PRK00549 competence damage-inducible protein A; Provisional
Probab=40.49 E-value=1.3e+02 Score=25.05 Aligned_cols=62 Identities=18% Similarity=0.300 Sum_probs=37.6
Q ss_pred EEEEcc-CCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845 32 SFTIER-EEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 32 ~~~i~~-EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~ 99 (110)
++.+.| -.=.|...|...+...++|.++-| |+ ...+.+|+...+. + .+..+++++.+.+.+.
T Consensus 182 ~l~~~gi~Es~l~~~L~~l~~~~~~v~ig~~--~~--~~~~~vrl~~~~~-~-~~~~~~~~~~~~~~i~ 244 (414)
T PRK00549 182 VLRFFGIGESQLATTLRDLIDNQTNPTIAPY--AK--DGEVTLRLTAKAR-S-EEEAEKLIDPLEEEIR 244 (414)
T ss_pred EEEEcCCCHHHHHHHHHHHHhcCCCCEEEEC--cc--CCEEEEEEEEecC-C-HHHHHHHHHHHHHHHH
Confidence 444444 234677888887778899998866 33 3567888887654 3 3444444444444333
No 48
>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=38.79 E-value=26 Score=20.44 Aligned_cols=25 Identities=20% Similarity=0.133 Sum_probs=12.0
Q ss_pred eeeEeeecCCCcceeEEEEccCCcch
Q 033845 17 KKVSYERDTKIINAASFTIEREEHTI 42 (110)
Q Consensus 17 ~Ki~~~~~~k~~n~~~~~i~~EDHTl 42 (110)
.++++.-.+.. ..+++.+.|+.+||
T Consensus 28 ~~v~v~~~~g~-~~l~i~v~g~~~~L 52 (54)
T PF03633_consen 28 EKVTVTLLSGD-APLTIKVYGEEVTL 52 (54)
T ss_dssp TEEEEEEEESS---EEEEETT-----
T ss_pred CEEEEEEccCC-ccEEEEECCCcccc
Confidence 34555555444 67899999999886
No 49
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.10 E-value=91 Score=25.09 Aligned_cols=40 Identities=23% Similarity=0.257 Sum_probs=33.8
Q ss_pred chHHHHHHHHhc-CCCeeeeeeeCCCCCCcceEEEEEeCCC
Q 033845 41 TIGNILRMQLHR-DENVLFAGYKLPHPLQYKIIVRIHTTSQ 80 (110)
Q Consensus 41 TlgNlLr~~L~~-~~~V~fAgY~vpHPl~~~~~lrIqT~~~ 80 (110)
++-|.|+...-+ -+.|.|+-|.+-||.-=-+.+..-|+..
T Consensus 93 ~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnk 133 (276)
T KOG2972|consen 93 GIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNK 133 (276)
T ss_pred HHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccH
Confidence 678888888876 5899999999999998778888888754
No 50
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=36.36 E-value=1.2e+02 Score=21.66 Aligned_cols=16 Identities=19% Similarity=0.216 Sum_probs=9.9
Q ss_pred CHHHHHHHHHHHHHHH
Q 033845 82 SPMQAYNQAINDLDKE 97 (110)
Q Consensus 82 ~P~~al~~a~~~l~~~ 97 (110)
+=-++|++|++++...
T Consensus 57 sF~d~Lk~Al~~VN~~ 72 (127)
T PRK12729 57 SFSEAMKNALTSVNDL 72 (127)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 4457777777665443
No 51
>KOG0758 consensus Mitochondrial carnitine-acylcarnitine carrier protein [Energy production and conversion]
Probab=36.09 E-value=51 Score=26.83 Aligned_cols=33 Identities=18% Similarity=0.343 Sum_probs=23.0
Q ss_pred eeeeeCCCCCCcceEEEEEeCCCCC---HHHHHHHHH
Q 033845 58 FAGYKLPHPLQYKIIVRIHTTSQSS---PMQAYNQAI 91 (110)
Q Consensus 58 fAgY~vpHPl~~~~~lrIqT~~~~~---P~~al~~a~ 91 (110)
.|+--|-||+ +.+.+|+||-.... ..+++++.+
T Consensus 25 ~~~vlVGhPf-DTvKVRlQt~~~~~y~~~~~c~~~t~ 60 (297)
T KOG0758|consen 25 AAQVLVGHPF-DTVKVRLQTQNTPVYKGTLDCVKKTL 60 (297)
T ss_pred hhhhhccCCc-cceEEeeeccCCCCcccHHHHHHHHH
Confidence 4667789999 67999999975422 355555544
No 52
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=35.57 E-value=32 Score=29.87 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=22.8
Q ss_pred ccCCcchHHHHHHHHhcCCCeeeee
Q 033845 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 4567899999999999999999998
No 53
>KOG0762 consensus Mitochondrial carrier protein [Energy production and conversion]
Probab=35.32 E-value=31 Score=27.84 Aligned_cols=26 Identities=42% Similarity=0.614 Sum_probs=21.4
Q ss_pred eeeeeCCCCCCcceEEEEEeCCCCCHH
Q 033845 58 FAGYKLPHPLQYKIIVRIHTTSQSSPM 84 (110)
Q Consensus 58 fAgY~vpHPl~~~~~lrIqT~~~~~P~ 84 (110)
.||--+-||+ +.+.+|.||.++.+|+
T Consensus 24 vAGVl~GhPl-DTvkVrlQtqs~~~Pq 49 (311)
T KOG0762|consen 24 VAGVLVGHPL-DTVKVRLQTQSSKSPQ 49 (311)
T ss_pred cceeeecCCc-ceeEEEEeccCCCCCc
Confidence 4888899999 5689999998877763
No 54
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=34.95 E-value=1.5e+02 Score=20.38 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033845 81 SSPMQAYNQAINDLDKELDTLKSAFEVK 108 (110)
Q Consensus 81 ~~P~~al~~a~~~l~~~~~~l~~~f~~~ 108 (110)
-++..|+..|++.|...+.-.++..++.
T Consensus 70 ~d~YaAID~a~dKLerqlrK~K~K~~~~ 97 (110)
T COG1544 70 EDMYAAIDLAIDKLERQLRKHKEKLKDH 97 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3899999999999999999998887653
No 55
>PRK01215 competence damage-inducible protein A; Provisional
Probab=34.34 E-value=2.3e+02 Score=22.20 Aligned_cols=68 Identities=13% Similarity=0.206 Sum_probs=37.8
Q ss_pred EEEEccCC-cchHHHHHHHHhcCCCeee--e--eeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033845 32 SFTIEREE-HTIGNILRMQLHRDENVLF--A--GYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (110)
Q Consensus 32 ~~~i~~ED-HTlgNlLr~~L~~~~~V~f--A--gY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~ 104 (110)
++.+.|-+ =+|.-.|.....+.|+|.+ + ||. +|+ ..+.+|+..++. + .+...+.++.+.+.+....++
T Consensus 183 ~~~~~Gi~Es~l~~~l~~l~~~~~~~~~~s~p~~~~-~~~--~~v~vrl~~~~~-~-~~~~~~~~~~~~~~i~~~~~~ 255 (264)
T PRK01215 183 SILVEGVMESDLAPYVKELVKKYDRVYVKSHPKGYE-VSK--PILEIQIAGSGE-R-EEEAKVKVEKVLEELKELIKK 255 (264)
T ss_pred EEEECCCCHHHHHHHHHHHHHhCCCCEEecCcccee-cCC--CeEEEEEEEecC-C-HHHHHHHHHHHHHHHHHHHHH
Confidence 45555533 4567777777777899988 4 344 343 567888876643 2 233333344444444444433
No 56
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=34.12 E-value=1.3e+02 Score=19.35 Aligned_cols=34 Identities=18% Similarity=0.261 Sum_probs=27.1
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 72 ~lrIqT~~~~~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 466665544 8999999999999999988887654
No 57
>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=33.67 E-value=1.2e+02 Score=22.78 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=26.4
Q ss_pred CcceeEEEEccCCcchHHHHHHHHhcCCCeeeee
Q 033845 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 3566666656788999999999999999999887
No 58
>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=33.42 E-value=1.3e+02 Score=19.05 Aligned_cols=34 Identities=24% Similarity=0.387 Sum_probs=26.1
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 72 ~lrIqT~~~~~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 34455443 48999999999999999988887653
No 59
>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=31.43 E-value=73 Score=19.93 Aligned_cols=24 Identities=13% Similarity=0.194 Sum_probs=16.3
Q ss_pred eEEEEEeCCCCCHHHHHHHHHHHH
Q 033845 71 IIVRIHTTSQSSPMQAYNQAINDL 94 (110)
Q Consensus 71 ~~lrIqT~~~~~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 356788888878889999999753
No 60
>PHA02781 hypothetical protein; Provisional
Probab=30.47 E-value=45 Score=21.46 Aligned_cols=26 Identities=31% Similarity=0.362 Sum_probs=21.0
Q ss_pred eeeEeeecCCCcceeEEEEccCCcch
Q 033845 17 KKVSYERDTKIINAASFTIEREEHTI 42 (110)
Q Consensus 17 ~Ki~~~~~~k~~n~~~~~i~~EDHTl 42 (110)
.||.++.|++..|-.++...-|.-|+
T Consensus 6 dkikitvdskignvvtisynlekiti 31 (78)
T PHA02781 6 DKIKITVDSKIGNVVTISYNLEKITI 31 (78)
T ss_pred ceEEEEeecccCcEEEEEeeeEEEEE
Confidence 47888889999999988877776664
No 61
>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=30.21 E-value=1.5e+02 Score=18.71 Aligned_cols=33 Identities=15% Similarity=0.351 Sum_probs=24.2
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 72 ~lrIqT~~~~~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 34444433 3899999999999999988776643
No 62
>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=28.55 E-value=1.5e+02 Score=24.23 Aligned_cols=50 Identities=8% Similarity=0.120 Sum_probs=39.9
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHH
Q 033845 40 HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92 (110)
Q Consensus 40 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 888888887777 8888999999999999999999887654 44444543
No 63
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=28.32 E-value=2e+02 Score=19.64 Aligned_cols=44 Identities=14% Similarity=0.129 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHH
Q 033845 43 GNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDL 94 (110)
Q Consensus 43 gNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l 94 (110)
.+.++..|+..|+++..+-.-+ .++.+.|++++. +-|-+.++.+
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~----GKlVVVie~~~~----~~l~~tie~i 63 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE----GKLVVVIEAEDS----ETLLETIESI 63 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC----ceEEEEEEcCch----HHHHHHHHHH
Confidence 4788999999999998776544 799999998864 4444444444
No 64
>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=28.22 E-value=1.3e+02 Score=17.38 Aligned_cols=47 Identities=11% Similarity=0.114 Sum_probs=30.4
Q ss_pred hHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHH
Q 033845 42 IGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 42 lgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~ 93 (110)
=.+.++..|.+.|+|.-+-....- +.+. |..+......+.+.+++++
T Consensus 12 C~~~v~~~l~~~~GV~~v~vd~~~---~~v~--v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 12 CAKKVEKALSKLPGVKSVKVDLET---KTVT--VTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp HHHHHHHHHHTSTTEEEEEEETTT---TEEE--EEESTTTSCHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCcEEEEECCC---CEEE--EEEecCCCCHHHHHHHHHH
Confidence 356788999999999777666542 4444 4444332233777777765
No 65
>PRK15202 type III secretion chaperone protein SigE; Provisional
Probab=28.07 E-value=2.2e+02 Score=20.08 Aligned_cols=75 Identities=20% Similarity=0.286 Sum_probs=50.3
Q ss_pred cCCCceeeEeeecCCCcceeEEEEccCCcchH------------HHHHHHHhcC--C----------CeeeeeeeCCCCC
Q 033845 12 VPEGTKKVSYERDTKIINAASFTIEREEHTIG------------NILRMQLHRD--E----------NVLFAGYKLPHPL 67 (110)
Q Consensus 12 l~~~~~Ki~~~~~~k~~n~~~~~i~~EDHTlg------------NlLr~~L~~~--~----------~V~fAgY~vpHPl 67 (110)
+|++++-+.+.. .+.+-|..++|+|- |-|.+.|.-| . .+..|-|+.|
T Consensus 16 ~~~depaliidd------di~IYfnes~~~lem~CPf~~LPdn~~~Lq~~LsLNYas~V~la~Dae~t~L~Al~rlp--- 86 (117)
T PRK15202 16 APEDEPALIIDD------DIQIYFNESDHTLEMCCPFMPLPDNILTLQHFLSLNYTSAVTLAADAENTALVALYRLP--- 86 (117)
T ss_pred CCCCCceEEecC------CeEEEEccCCcchhccCCcccCCccHHHHHHHHhhcccCceEEEEcCCCceEEEeeecC---
Confidence 456777776654 48999999999973 4566666544 2 2333445544
Q ss_pred CcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033845 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEV 107 (110)
Q Consensus 68 ~~~~~lrIqT~~~~~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 3345566677888888888888888764
No 66
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=27.94 E-value=1e+02 Score=23.86 Aligned_cols=38 Identities=18% Similarity=0.220 Sum_probs=27.5
Q ss_pred eEEEEEeCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033845 71 IIVRIHTTSQS--SPMQAYNQAINDLDKELDTLKSAFEVK 108 (110)
Q Consensus 71 ~~lrIqT~~~~--~P~~al~~a~~~l~~~~~~l~~~f~~~ 108 (110)
++|-+.|.++. .|++++..++..+++.+..=-.+.++.
T Consensus 6 ~~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v 45 (207)
T COG4245 6 CYLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERV 45 (207)
T ss_pred EEEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhhee
Confidence 56778887654 789999999999888876543344433
No 67
>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=27.73 E-value=1.4e+02 Score=18.75 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=18.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q 033845 81 SSPMQAYNQAINDLDKELDTLK 102 (110)
Q Consensus 81 ~~P~~al~~a~~~l~~~~~~l~ 102 (110)
.+...||..|++.|...+...+
T Consensus 70 ~d~~~Aid~a~~kl~rqL~k~k 91 (93)
T cd00552 70 EDLYAAIDLAVDKLERQLRKYK 91 (93)
T ss_pred CCHHHHHHHHHHHHHHHHHHhc
Confidence 4889999999999988887654
No 68
>PLN02231 alanine transaminase
Probab=27.57 E-value=2.8e+02 Score=23.80 Aligned_cols=58 Identities=7% Similarity=-0.026 Sum_probs=38.0
Q ss_pred HHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 46 LRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 46 Lr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~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 445566666666553332223334456777652 5679999999999988888877764
No 69
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=27.48 E-value=1e+02 Score=21.53 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033845 82 SPMQAYNQAINDLDKELDTLKSAFEVK 108 (110)
Q Consensus 82 ~P~~al~~a~~~l~~~~~~l~~~f~~~ 108 (110)
+|.+.|++-=+.+.+.++.+++.|..+
T Consensus 84 ~P~k~leei~~~i~keiEelEk~~k~e 110 (113)
T COG5625 84 PPPKPLEEIEEEIMKEIEELEKEFKNE 110 (113)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 678888888899999999999999765
No 70
>PRK04207 glyceraldehyde-3-phosphate dehydrogenase; Provisional
Probab=26.94 E-value=2.6e+02 Score=22.54 Aligned_cols=51 Identities=16% Similarity=0.200 Sum_probs=37.4
Q ss_pred cchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHH
Q 033845 40 HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 40 HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~ 93 (110)
|+ |--++..+-.. +|.....+||-+.-+-.-+.++++...+. +.+.+++++
T Consensus 193 ~~-g~~v~~vlp~l-~i~~~avrVPv~~gh~~~v~v~l~~~~t~-eev~~~l~~ 243 (341)
T PRK04207 193 HH-GPDVKTVLPDL-DITTMAVKVPTTLMHMHSVNVELKKPVTK-EEVLEALEN 243 (341)
T ss_pred Cc-hhHHHhhCCCC-ceEEEEEEcCCCCceEEEEEEEECCCCCH-HHHHHHHHh
Confidence 44 66666666332 38888899999999999999999987665 445555553
No 71
>PHA02766 hypothetical protein; Provisional
Probab=26.90 E-value=58 Score=20.62 Aligned_cols=50 Identities=26% Similarity=0.305 Sum_probs=31.0
Q ss_pred eeEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHH
Q 033845 30 AASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAI 91 (110)
Q Consensus 30 ~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~ 91 (110)
.++|+|..||.-- |.+. -|+.| --|+.++++++|.|+.-.+-.+|+---+
T Consensus 16 kisfeineedyqq-------liel---afsqf--iyplndnieikintkeladnekallyei 65 (73)
T PHA02766 16 KISFEINEEDYQQ-------LIEL---AFSQF--IYPLNDNIEIKINTKELADNEKALLYEI 65 (73)
T ss_pred EEEEEECHHHHHH-------HHHH---HHHhh--eeeCCCceEEEechHhhccchhhHhHhh
Confidence 4678888888531 1111 12222 3479999999999986555556654433
No 72
>KOG0359 consensus Chaperonin complex component, TCP-1 zeta subunit (CCT6) [Posttranslational modification, protein turnover, chaperones]
Probab=26.48 E-value=75 Score=27.60 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=30.7
Q ss_pred CceeeEeeecCCCcceeEEEEccCC-cchH---HHHHHHHhc
Q 033845 15 GTKKVSYERDTKIINAASFTIEREE-HTIG---NILRMQLHR 52 (110)
Q Consensus 15 ~~~Ki~~~~~~k~~n~~~~~i~~ED-HTlg---NlLr~~L~~ 52 (110)
||.|.++.+..+.|+++|+-|.|-. ||+. .++|..|..
T Consensus 348 GEEkfTFIE~~~~p~S~TiLikgpnkht~tQikdairdglra 389 (520)
T KOG0359|consen 348 GEEKFTFIEKCNNPSSVTILIKGPNKHTITQIKDAIRDGLRA 389 (520)
T ss_pred cceeeEeeecCCCCcceEEEEeCCccchHHHHHHHHhhHHHH
Confidence 7999999999999999999998765 8875 345555544
No 73
>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=26.46 E-value=1.2e+02 Score=16.46 Aligned_cols=21 Identities=33% Similarity=0.512 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 033845 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 455666666666666666664
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=25.87 E-value=1.7e+02 Score=25.29 Aligned_cols=30 Identities=20% Similarity=0.363 Sum_probs=24.0
Q ss_pred eEEEEcc-CCcchHHHHHHHHhcCCCeeeee
Q 033845 31 ASFTIER-EEHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 31 ~~~~i~~-EDHTlgNlLr~~L~~~~~V~fAg 60 (110)
..+.+.. ...|+.++|+..|.++|+|.+.|
T Consensus 362 ~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vG 392 (564)
T TIGR02538 362 NQVNVNPKIGLTFAAALRSFLRQDPDIIMVG 392 (564)
T ss_pred eEEEeccccCCCHHHHHHHHhccCCCEEEeC
Confidence 3445543 34799999999999999999988
No 75
>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=25.59 E-value=1.1e+02 Score=19.36 Aligned_cols=21 Identities=10% Similarity=0.023 Sum_probs=16.9
Q ss_pred EEEEeCCCCCHHHHHHHHHHH
Q 033845 73 VRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 73 lrIqT~~~~~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 76
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=24.55 E-value=51 Score=23.76 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=21.4
Q ss_pred HHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEe
Q 033845 45 ILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHT 77 (110)
Q Consensus 45 lLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT 77 (110)
.+=.++.++|+|+|||....- .++|+.-
T Consensus 48 ~~yKqik~np~vefcg~~kdg-----~~vrlrg 75 (132)
T COG5015 48 PYYKQIKKNPEVEFCGMDKDG-----VMVRLRG 75 (132)
T ss_pred HHHHHHhhCCCeEEEEecCCc-----eEEEEee
Confidence 466789999999999987654 5666554
No 77
>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=24.30 E-value=2.3e+02 Score=21.84 Aligned_cols=32 Identities=19% Similarity=0.367 Sum_probs=24.5
Q ss_pred ceeEEEEccC-CcchHHHHHHHHhcCCCeeeee
Q 033845 29 NAASFTIERE-EHTIGNILRMQLHRDENVLFAG 60 (110)
Q Consensus 29 n~~~~~i~~E-DHTlgNlLr~~L~~~~~V~fAg 60 (110)
+...+.+..+ +-|+..+|+..|..+|+|.+.|
T Consensus 124 ~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vg 156 (264)
T cd01129 124 GINQVQVNEKAGLTFARGLRAILRQDPDIIMVG 156 (264)
T ss_pred CceEEEeCCcCCcCHHHHHHHHhccCCCEEEec
Confidence 3334455433 4699999999999999999887
No 78
>COG2033 Desulfoferrodoxin [Energy production and conversion]
Probab=23.39 E-value=57 Score=23.37 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=8.8
Q ss_pred eeeeCCCCCCcc
Q 033845 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 899999866
No 79
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=23.10 E-value=2.8e+02 Score=21.89 Aligned_cols=69 Identities=12% Similarity=0.116 Sum_probs=41.5
Q ss_pred eEEEEccCC-cchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033845 31 ASFTIEREE-HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102 (110)
Q Consensus 31 ~~~~i~~ED-HTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~ 102 (110)
-++.+.|-. =.|+-.|+......|+|.++.|-...-.... .|.|+... .-.++++.+++.+...+....
T Consensus 181 ~~~~~~gi~ES~la~~L~~i~~~~~~~~i~s~p~~~~~~~~-~~~i~~~~--~~~~~~~~~~~~~~~~i~~~~ 250 (255)
T COG1058 181 RVLRVFGIGESSLAPTLKDLQDEQPNVTIASYPKDGEVRLR-ELVIRAEA--RDEEEADALLRWLEGRLRARG 250 (255)
T ss_pred EEEEEcCCChHHHHHHHHHHHhcCCCCEEEecCCCCceecc-ceEEEEec--CCHHHHHHHHHHHHHHHHHhh
Confidence 445554333 3578888888888999998887554433221 34466543 235666666666666555443
No 80
>PRK15197 secreted effector protein PipB; Provisional
Probab=22.97 E-value=4e+02 Score=21.41 Aligned_cols=42 Identities=5% Similarity=0.080 Sum_probs=26.1
Q ss_pred eeeeeeeC----CCCC---CcceEEEEEeCCCCCHHHHHHHHHHHHHHH
Q 033845 56 VLFAGYKL----PHPL---QYKIIVRIHTTSQSSPMQAYNQAINDLDKE 97 (110)
Q Consensus 56 V~fAgY~v----pHPl---~~~~~lrIqT~~~~~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 77999998 3332 455777777665555556666666554444
No 81
>PF14185 SpoIISB_antitox: Antitoxin SpoIISB, type II toxin-antitoxin system ; PDB: 3O6Q_B.
Probab=22.85 E-value=15 Score=22.69 Aligned_cols=15 Identities=40% Similarity=0.789 Sum_probs=4.8
Q ss_pred hcCCCeeeeeeeC-CC
Q 033845 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 3456788999987 55
No 82
>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=22.82 E-value=1.1e+02 Score=19.06 Aligned_cols=23 Identities=9% Similarity=0.021 Sum_probs=17.0
Q ss_pred eEEEEEeCCCCCHHHHHHHHHHH
Q 033845 71 IIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 71 ~~lrIqT~~~~~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 34456777888999999999863
No 83
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=22.35 E-value=1.8e+02 Score=22.78 Aligned_cols=27 Identities=7% Similarity=0.212 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 80 QSSPMQAYNQAINDLDKELDTLKSAFE 106 (110)
Q Consensus 80 ~~~P~~al~~a~~~l~~~~~~l~~~f~ 106 (110)
+++|..||++|..+....|..++....
T Consensus 200 giDpE~ALr~a~~KF~~Rf~~~E~~~~ 226 (248)
T TIGR00444 200 KTDAEIALQKANEKFERRFREVERIVA 226 (248)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999999987654
No 84
>smart00455 RBD Raf-like Ras-binding domain.
Probab=22.23 E-value=2.1e+02 Score=17.83 Aligned_cols=23 Identities=9% Similarity=0.085 Sum_probs=18.2
Q ss_pred eEEEEEeCCCCCHHHHHHHHHHH
Q 033845 71 IIVRIHTTSQSSPMQAYNQAIND 93 (110)
Q Consensus 71 ~~lrIqT~~~~~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 34567777888999999999874
No 85
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=21.51 E-value=2.7e+02 Score=18.84 Aligned_cols=47 Identities=23% Similarity=0.162 Sum_probs=38.0
Q ss_pred cCCCceeeEeeecCCCc-ceeEEEEccCCcchHHHHHHHHhcCCCeee
Q 033845 12 VPEGTKKVSYERDTKII-NAASFTIEREEHTIGNILRMQLHRDENVLF 58 (110)
Q Consensus 12 l~~~~~Ki~~~~~~k~~-n~~~~~i~~EDHTlgNlLr~~L~~~~~V~f 58 (110)
..+-.+++.+.+.||.. +++++.|.-++--=--.|-.+|-+.+.|..
T Consensus 41 p~~~~~~~~~k~SSkGnY~svsI~i~A~~~EQ~e~ly~eL~~~~~Vkm 88 (90)
T COG2921 41 PGDYTPRVSWKPSSKGNYLSVSITIRATNIEQVEALYRELRKHEIVKM 88 (90)
T ss_pred CcccCceeeeccCCCCceEEEEEEEEECCHHHHHHHHHHHhhCCceEE
Confidence 34557889999987754 778899999998888888889999998875
No 86
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=21.50 E-value=1.8e+02 Score=24.07 Aligned_cols=54 Identities=19% Similarity=0.344 Sum_probs=40.7
Q ss_pred HHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033845 44 NILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (110)
Q Consensus 44 NlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~ 104 (110)
|.+|+.=++ ++.+-|-.-.| ..+.|.+.|...|...+.+|+.-|...|..+++.
T Consensus 283 e~~R~ee~~--d~V~LgrvrdH-----fIFsvestgal~p~~lf~eavkvle~Kc~al~~~ 336 (338)
T KOG1521|consen 283 EVLRHEELK--DKVQLGRVRDH-----FIFSVESTGALKPEVLFEEAVKVLEEKCRALRDE 336 (338)
T ss_pred HHhccHHhh--hheeeccccce-----EEEEeecccCCCchhhHHHHHHHHHHHHHHHhhc
Confidence 555553333 33445555555 7889999999999999999999999999988765
No 87
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=21.00 E-value=1.3e+02 Score=24.16 Aligned_cols=37 Identities=14% Similarity=0.160 Sum_probs=30.1
Q ss_pred eeeEeeecCCCcceeEEEEccCCcchHHHHHHHHhc-CCC
Q 033845 17 KKVSYERDTKIINAASFTIEREEHTIGNILRMQLHR-DEN 55 (110)
Q Consensus 17 ~Ki~~~~~~k~~n~~~~~i~~EDHTlgNlLr~~L~~-~~~ 55 (110)
+.|++.+- .++.+.|++.+-|=.++|.||-.++. .|-
T Consensus 6 p~v~I~El--t~d~vkF~L~nTdlsvANsLRRV~iaEvPT 43 (285)
T KOG1522|consen 6 PTVKIREL--TDDNVKFVLSNTDLSVANSLRRVMIAEVPT 43 (285)
T ss_pred CceEEEec--CCCceEEEEecChHHHHHHHHHHHHhcCce
Confidence 46667654 67889999999999999999998876 454
No 88
>PTZ00377 alanine aminotransferase; Provisional
Probab=20.98 E-value=4.5e+02 Score=21.71 Aligned_cols=57 Identities=7% Similarity=0.086 Sum_probs=34.9
Q ss_pred HHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033845 46 LRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (110)
Q Consensus 46 Lr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f 105 (110)
+...+++..+|.+.....-.+....-.+||-.. .+.+.+++|++.|.+.+..+.++|
T Consensus 424 ~~~~ll~~~gV~v~pG~~F~~~~~~~~~Rls~~---~~~e~l~~~l~rl~~~~~~~~~~~ 480 (481)
T PTZ00377 424 YCLELLESTGIVVVPGSGFGQKPGTYHFRITIL---PPEEQIEEMVKKIKEFHESFMKKY 480 (481)
T ss_pred HHHHHHHHcCEEEeCCcccCCCCCCCEEEEEEC---CCHHHHHHHHHHHHHHHHHHHHhh
Confidence 344566666776653332222222346777764 346889999999988777665554
No 89
>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=20.88 E-value=1.9e+02 Score=16.93 Aligned_cols=45 Identities=11% Similarity=0.026 Sum_probs=28.2
Q ss_pred eEEEEccCCcchHHHHHHHHhcCCCeeeeeeeCCCCCCcceEEEEEeC
Q 033845 31 ASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTT 78 (110)
Q Consensus 31 ~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~ 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 45566666667777766555556566543 44333 23699999995
No 90
>PLN02150 terpene synthase/cyclase family protein
Probab=20.75 E-value=1.6e+02 Score=19.50 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhC
Q 033845 88 NQAINDLDKELDTLKSAFEVKHL 110 (110)
Q Consensus 88 ~~a~~~l~~~~~~l~~~f~~~~~ 110 (110)
++|.+.+.+.+++..+.++.+++
T Consensus 22 eeA~~~i~~li~~~WK~iN~e~l 44 (96)
T PLN02150 22 EEAVSELKKMIRDNYKIVMEEFL 44 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Confidence 36777788888888888777764
No 91
>cd07353 harmonin_N N-terminal protein-binding module of harmonin. Harmonin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. Harmonin contains a single copy of this domain, which is found at the N-terminus of all three harmonin isoform classes (a, b and c), and which preceeds the first PDZ protein-binding domain, PDZ1. This harmonin_N domain binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network.
Probab=20.73 E-value=36 Score=22.27 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=12.2
Q ss_pred CCCCccccceecCCCceee
Q 033845 1 MNAPDRYERFVVPEGTKKV 19 (110)
Q Consensus 1 mn~p~~~~~~~l~~~~~Ki 19 (110)
+|.|+|++|| ++-|++
T Consensus 49 IN~P~R~pLf---d~IR~l 64 (79)
T cd07353 49 INEPSRLPLF---DAIRPL 64 (79)
T ss_pred hCCccccchH---HHHHhh
Confidence 5899999999 555554
No 92
>cd04402 RhoGAP_ARHGAP20 RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=20.43 E-value=20 Score=26.37 Aligned_cols=51 Identities=14% Similarity=0.178 Sum_probs=30.4
Q ss_pred CccccceecCCCceeeEeeecCCCcceeEEEEccCC-cchHHHHHHHHhcCCC
Q 033845 4 PDRYERFVVPEGTKKVSYERDTKIINAASFTIEREE-HTIGNILRMQLHRDEN 55 (110)
Q Consensus 4 p~~~~~~~l~~~~~Ki~~~~~~k~~n~~~~~i~~ED-HTlgNlLr~~L~~~~~ 55 (110)
++.--+|-++.+..++...+. +.++...+.+.+.| ||++++|+..|.+.|+
T Consensus 31 ~~~eGiFR~~g~~~~i~~l~~-~~~~~~~~~~~~~~~~~va~~lK~flreLpe 82 (192)
T cd04402 31 PSTEGIFRRSANAKACKELKE-KLNSGVEVDLKAEPVLLLASVLKDFLRNIPG 82 (192)
T ss_pred CCCCCeeeCCCcHHHHHHHHH-HHhCCCCCCCccCCHHHHHHHHHHHHHhCCC
Confidence 344446666665554433332 11111223345667 9999999999999876
No 93
>PF14318 Mononeg_mRNAcap: Mononegavirales mRNA-capping region V
Probab=20.25 E-value=56 Score=25.27 Aligned_cols=25 Identities=24% Similarity=0.531 Sum_probs=19.6
Q ss_pred chHHHHHHHHhcCCCeeeeeeeCCCCCC
Q 033845 41 TIGNILRMQLHRDENVLFAGYKLPHPLQ 68 (110)
Q Consensus 41 TlgNlLr~~L~~~~~V~fAgY~vpHPl~ 68 (110)
+++..||..-+ +=...|-.+|||+|
T Consensus 5 ~~A~~LR~~SW---Gr~I~GvT~P~P~E 29 (245)
T PF14318_consen 5 DLADYLRRKSW---GRPIIGVTVPHPIE 29 (245)
T ss_pred HHHHHHHHhcC---CCeEEEEeCCCHHH
Confidence 46777888888 45578999999985
No 94
>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=20.19 E-value=1.6e+02 Score=22.81 Aligned_cols=35 Identities=9% Similarity=0.115 Sum_probs=20.5
Q ss_pred eeeeeCCCCCCcceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033845 58 FAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (110)
Q Consensus 58 fAgY~vpHPl~~~~~lrIqT~~~~~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 5789999975432 2332344556666666555543
No 95
>PF09137 Glucodextran_N: Glucodextranase, domain N; InterPro: IPR015220 Glucodextranase domain N, uniquely found in bacterial and archaeal glucoamylases and glucodextranases, adopts a structure consisting of 17 antiparallel beta-strands. These beta-strands are divided into two beta-sheets, and one of the beta-sheets is wrapped by an extended polypeptide, which appears to stabilise the domain. This domain, together with glycoside hydrolase domain A (IPR011613 from INTERPRO), is mainly involved with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism []. ; PDB: 1UG9_A 1ULV_A 1LF6_B 1LF9_A.
Probab=20.17 E-value=92 Score=24.81 Aligned_cols=38 Identities=11% Similarity=0.134 Sum_probs=30.0
Q ss_pred ceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033845 70 KIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEVKH 109 (110)
Q Consensus 70 ~~~lrIqT~~~~~P~~al~~a~~~l~~~~~~l~~~f~~~~ 109 (110)
...|-+-- +.++.+|+..|...|..-++.+++.|...|
T Consensus 225 ~f~laLgF--G~~~~~A~~~A~asL~~gf~~~~~~Y~~~W 262 (269)
T PF09137_consen 225 EFTLALGF--GDSAEEAAATARASLARGFEEVLARYNGGW 262 (269)
T ss_dssp EEEEEEEE--ESSHHHHHHHHHHHHCC-HHHHHHHHHHHH
T ss_pred eEEEEEEc--CCCHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence 34444443 237899999999999999999999999998
No 96
>PHA02729 hypothetical protein; Provisional
Probab=20.02 E-value=1.4e+02 Score=20.23 Aligned_cols=59 Identities=10% Similarity=0.185 Sum_probs=43.7
Q ss_pred CCccccceecCCC-ceeeEeeecCC-CcceeEEEEccCCcchHHHHHHHHhcCCCeeeeee
Q 033845 3 APDRYERFVVPEG-TKKVSYERDTK-IINAASFTIEREEHTIGNILRMQLHRDENVLFAGY 61 (110)
Q Consensus 3 ~p~~~~~~~l~~~-~~Ki~~~~~~k-~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY 61 (110)
-|++-|||.|... .+-|.|..+.. +.+.+=+=...+|.++..=|......+-+-.|--|
T Consensus 7 ~~~~~elf~L~N~dgkniAW~~~k~~~~~diW~P~tedDYkFL~~LV~~v~~n~~tk~dYY 67 (94)
T PHA02729 7 FSEARELFSLTNDDNRNIAWDTDKLDDDTDIWTPVTEDDYKFLSRLVLMAKLNRDTVFDYY 67 (94)
T ss_pred ccchhhhheeeccCCccccccccccccCCceeecCcchHHHHHHHHHHHHhhccccceeeE
Confidence 4888899988765 45599988876 66677777788999999888888776544444334
Done!