Query 033562
Match_columns 116
No_of_seqs 102 out of 484
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 03:42:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033562.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033562hhsearch_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 8.8E-44 1.9E-48 249.9 12.7 111 1-111 1-111 (117)
2 cd06926 RNAP_II_RPB11 RPB11 su 100.0 5.1E-39 1.1E-43 220.2 11.7 93 13-105 1-93 (93)
3 PF13656 RNA_pol_L_2: RNA poly 100.0 2E-36 4.3E-41 200.9 9.1 77 29-105 1-77 (77)
4 cd07029 RNAP_I_III_AC19 AC19 s 100.0 6.9E-36 1.5E-40 201.8 10.3 82 24-105 4-85 (85)
5 PRK01146 DNA-directed RNA poly 100.0 8.9E-35 1.9E-39 196.4 10.4 79 25-103 7-85 (85)
6 cd06927 RNAP_L L subunit of Ar 100.0 1.8E-34 3.8E-39 194.1 10.0 79 25-103 5-83 (83)
7 cd07027 RNAP_RPB11_like RPB11 100.0 2.8E-34 6.2E-39 193.1 10.2 78 25-102 5-82 (83)
8 COG1761 RPB11 DNA-directed RNA 100.0 1.2E-33 2.5E-38 195.8 12.7 97 16-113 2-98 (99)
9 KOG3438 DNA-directed RNA polym 100.0 4.1E-34 8.9E-39 198.0 10.2 89 27-115 14-102 (105)
10 cd00460 RNAP_RPB11_RPB3 RPB11 99.9 5.9E-26 1.3E-30 152.8 9.7 76 25-101 5-86 (86)
11 PF01193 RNA_pol_L: RNA polyme 99.7 2.1E-17 4.5E-22 105.9 5.2 65 31-99 1-66 (66)
12 PRK14979 DNA-directed RNA poly 95.6 0.06 1.3E-06 41.4 7.0 51 53-107 138-188 (195)
13 cd06928 RNAP_alpha_NTD N-termi 95.4 0.03 6.6E-07 43.2 4.9 45 55-99 163-213 (215)
14 cd07028 RNAP_RPB3_like RPB3 su 95.3 0.057 1.2E-06 41.8 5.9 52 51-103 160-211 (212)
15 TIGR02027 rpoA DNA-directed RN 95.1 0.072 1.6E-06 43.1 6.2 49 55-103 154-208 (297)
16 smart00662 RPOLD RNA polymeras 94.9 0.059 1.3E-06 41.7 5.2 45 56-100 163-223 (224)
17 PRK05182 DNA-directed RNA poly 94.3 0.13 2.8E-06 41.9 6.0 49 55-103 171-225 (310)
18 PRK00783 DNA-directed RNA poly 94.1 0.064 1.4E-06 42.1 3.8 36 18-55 2-38 (263)
19 CHL00013 rpoA RNA polymerase a 94.1 0.13 2.8E-06 42.4 5.6 49 55-103 170-223 (327)
20 cd07030 RNAP_D D subunit of Ar 93.0 0.13 2.8E-06 40.3 3.8 36 18-55 2-38 (259)
21 cd07031 RNAP_II_RPB3 RPB3 subu 93.0 0.21 4.5E-06 39.9 5.0 53 55-107 201-264 (265)
22 CHL00013 rpoA RNA polymerase a 91.9 0.31 6.6E-06 40.2 4.8 47 19-65 10-61 (327)
23 PRK05182 DNA-directed RNA poly 91.8 0.38 8.3E-06 39.2 5.2 47 18-64 8-59 (310)
24 cd06928 RNAP_alpha_NTD N-termi 91.1 0.32 7E-06 37.5 3.9 39 26-64 6-49 (215)
25 cd07028 RNAP_RPB3_like RPB3 su 91.0 0.26 5.6E-06 38.2 3.3 31 26-56 8-39 (212)
26 cd07031 RNAP_II_RPB3 RPB3 subu 90.2 0.63 1.4E-05 37.1 4.9 39 18-58 2-41 (265)
27 PRK14979 DNA-directed RNA poly 89.9 0.6 1.3E-05 35.9 4.4 37 23-60 8-45 (195)
28 smart00662 RPOLD RNA polymeras 89.8 0.44 9.6E-06 36.8 3.7 33 31-63 2-35 (224)
29 COG0202 RpoA DNA-directed RNA 89.2 0.8 1.7E-05 37.6 5.0 45 19-63 7-54 (317)
30 PRK00783 DNA-directed RNA poly 89.1 1.2 2.6E-05 35.0 5.7 41 67-107 221-261 (263)
31 cd07030 RNAP_D D subunit of Ar 86.6 1.8 3.9E-05 33.9 5.3 37 68-104 222-258 (259)
32 cd07032 RNAP_I_II_AC40 AC40 su 83.9 3 6.5E-05 33.9 5.5 37 67-103 254-290 (291)
33 TIGR02027 rpoA DNA-directed RN 81.8 1.7 3.7E-05 35.2 3.4 29 36-64 11-40 (297)
34 COG2805 PilT Tfp pilus assembl 80.3 1.4 3E-05 36.8 2.4 24 38-61 183-206 (353)
35 PRK02261 methylaspartate mutas 67.2 6.8 0.00015 28.1 3.0 38 27-64 3-42 (137)
36 cd02067 B12-binding B12 bindin 62.8 21 0.00046 24.0 4.7 34 31-64 3-38 (119)
37 cd02070 corrinoid_protein_B12- 62.0 19 0.0004 27.0 4.7 39 28-66 83-123 (201)
38 TIGR02370 pyl_corrinoid methyl 61.1 20 0.00044 26.9 4.7 39 28-66 85-125 (197)
39 cd02071 MM_CoA_mut_B12_BD meth 60.1 26 0.00057 24.0 4.9 26 31-56 3-28 (122)
40 cd02069 methionine_synthase_B1 58.8 22 0.00047 27.3 4.6 39 28-66 89-129 (213)
41 cd04905 ACT_CM-PDT C-terminal 57.1 46 0.001 20.8 6.4 68 30-99 3-71 (80)
42 PF06657 Cep57_MT_bd: Centroso 55.6 50 0.0011 21.7 5.4 34 79-112 7-40 (79)
43 PF05986 ADAM_spacer1: ADAM-TS 47.9 62 0.0013 22.2 5.1 71 6-78 16-100 (114)
44 PF04368 DUF507: Protein of un 45.7 1E+02 0.0023 23.4 6.4 34 82-115 124-157 (183)
45 KOG1522 RNA polymerase II, sub 45.7 47 0.001 27.0 4.7 77 30-110 176-270 (285)
46 COG0202 RpoA DNA-directed RNA 45.6 41 0.00088 27.7 4.5 40 68-107 187-226 (317)
47 COG1544 Ribosome-associated pr 41.2 1.2E+02 0.0027 21.1 6.4 43 66-108 47-97 (110)
48 COG1027 AspA Aspartate ammonia 40.8 60 0.0013 28.2 4.9 67 42-114 112-181 (471)
49 KOG2972 Uncharacterized conser 40.4 79 0.0017 25.7 5.2 51 41-91 93-144 (276)
50 PHA02766 hypothetical protein; 39.4 27 0.00058 22.4 2.0 50 30-91 16-65 (73)
51 COG2804 PulE Type II secretory 39.3 26 0.00055 30.8 2.5 26 36-61 310-335 (500)
52 PRK00549 competence damage-ind 38.9 1.4E+02 0.0031 25.1 6.9 37 40-80 191-227 (414)
53 cd07032 RNAP_I_II_AC40 AC40 su 38.3 50 0.0011 26.9 3.9 34 18-53 2-35 (291)
54 PF00437 T2SE: Type II/IV secr 36.3 1.1E+02 0.0023 23.5 5.3 34 27-60 171-204 (270)
55 PRK12729 fliE flagellar hook-b 35.2 60 0.0013 23.6 3.5 18 50-68 9-26 (127)
56 COG5211 SSU72 RNA polymerase I 32.7 2.2E+02 0.0048 21.8 6.3 80 35-114 71-183 (197)
57 PHA02781 hypothetical protein; 30.3 43 0.00093 21.8 1.9 26 17-42 6-31 (78)
58 PF11598 COMP: Cartilage oligo 30.2 1.3E+02 0.0027 18.0 4.7 29 83-111 2-30 (45)
59 KOG2070 Guanine nucleotide exc 30.1 1.2E+02 0.0027 27.2 5.2 52 61-112 583-646 (661)
60 PF13851 GAS: Growth-arrest sp 29.8 1.1E+02 0.0023 23.4 4.3 30 85-114 110-139 (201)
61 COG4495 Uncharacterized protei 29.2 1E+02 0.0022 21.8 3.7 50 57-109 38-93 (109)
62 TIGR01546 GAPDH-II_archae glyc 27.8 1.6E+02 0.0035 24.3 5.3 51 40-93 190-240 (333)
63 TIGR00741 yfiA ribosomal subun 27.1 1.7E+02 0.0038 18.6 5.0 33 72-105 60-92 (95)
64 cd00330 phosphagen_kinases Pho 27.0 3.1E+02 0.0068 21.5 7.2 19 73-91 109-128 (236)
65 cd01129 PulE-GspE PulE/GspE Th 26.8 1.9E+02 0.0041 22.6 5.4 32 29-60 124-156 (264)
66 TIGR02538 type_IV_pilB type IV 26.8 1.5E+02 0.0033 25.9 5.3 30 31-60 362-392 (564)
67 COG1058 CinA Predicted nucleot 26.7 3.4E+02 0.0073 21.8 6.8 71 30-103 180-251 (255)
68 PF03633 Glyco_hydro_65C: Glyc 26.6 46 0.00099 19.6 1.5 23 19-42 30-52 (54)
69 PRK15197 secreted effector pro 26.5 3E+02 0.0066 22.4 6.6 42 56-97 84-132 (291)
70 COG2033 Desulfoferrodoxin [Ene 26.3 46 0.001 24.1 1.7 11 59-70 57-67 (126)
71 PRK10470 ribosome hibernation 25.1 2E+02 0.0043 18.7 5.1 33 72-105 60-92 (95)
72 PF11470 TUG-UBL1: GLUT4 regul 25.0 1.1E+02 0.0024 19.4 3.1 23 72-94 8-30 (65)
73 PF00403 HMA: Heavy-metal-asso 24.9 1.5E+02 0.0033 17.2 5.6 47 42-93 12-58 (62)
74 PRK01215 competence damage-ind 24.8 2.6E+02 0.0056 22.2 5.8 45 32-79 183-232 (264)
75 PF04263 TPK_catalytic: Thiami 24.3 21 0.00046 25.1 -0.4 16 37-52 97-112 (123)
76 COG0365 Acs Acyl-coenzyme A sy 24.2 4.3E+02 0.0093 23.3 7.5 58 35-93 422-482 (528)
77 PF02482 Ribosomal_S30AE: Sigm 23.4 2.1E+02 0.0045 18.2 4.6 32 72-104 62-93 (97)
78 cd00552 RaiA RaiA ("ribosome-a 23.3 1.8E+02 0.004 18.4 4.0 22 81-102 70-91 (93)
79 PF11348 DUF3150: Protein of u 23.0 1.2E+02 0.0027 24.0 3.7 25 82-106 81-105 (257)
80 TIGR02065 ECX1 archaeal exosom 22.9 3.4E+02 0.0074 20.5 8.4 76 30-112 153-229 (230)
81 PF14185 SpoIISB_antitox: Anti 22.6 17 0.00038 22.7 -0.9 16 50-65 20-36 (56)
82 PLN02231 alanine transaminase 22.4 3.6E+02 0.0079 23.4 6.7 57 46-105 476-532 (534)
83 PF02700 PurS: Phosphoribosylf 22.4 1.6E+02 0.0034 19.3 3.5 24 71-94 3-28 (80)
84 smart00800 uDENN Domain always 22.3 1.8E+02 0.0039 18.8 3.8 36 3-39 42-77 (89)
85 PRK05783 hypothetical protein; 22.2 1.5E+02 0.0032 19.8 3.4 25 70-94 4-30 (84)
86 PRK15202 type III secretion ch 21.8 3.1E+02 0.0067 19.6 8.7 75 13-108 17-115 (117)
87 PF05465 Halo_GVPC: Halobacter 21.7 1.6E+02 0.0034 16.2 3.7 28 85-112 2-29 (32)
88 KOG0758 Mitochondrial carnitin 21.1 1.4E+02 0.003 24.7 3.7 34 58-92 25-61 (297)
89 PF12010 DUF3502: Domain of un 20.9 3.1E+02 0.0067 19.2 5.1 35 79-113 95-130 (134)
90 COG5625 Predicted transcriptio 20.6 1.7E+02 0.0037 20.7 3.6 52 42-108 57-110 (113)
91 PTZ00377 alanine aminotransfer 20.5 4.5E+02 0.0097 22.0 6.8 56 47-105 425-480 (481)
92 KOG1507 Nucleosome assembly pr 20.2 1.2E+02 0.0026 25.6 3.2 28 88-115 79-106 (358)
93 PF02777 Sod_Fe_C: Iron/mangan 20.0 1.2E+02 0.0026 20.3 2.7 30 82-111 2-31 (106)
No 1
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=8.8e-44 Score=249.92 Aligned_cols=111 Identities=54% Similarity=0.849 Sum_probs=110.0
Q ss_pred CCCCccccceeeCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCC
Q 033562 1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ 80 (116)
Q Consensus 1 ~n~p~~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~ 80 (116)
||||+|||+|+|.+|++||++..|+|++|++.|+|.+|||||||+|+.+|+++|+|.||||++|||++.++.+||||..+
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 CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033562 81 SSPMQAYNQAINDLDKELDTLKSAFEAELAK 111 (116)
Q Consensus 81 ~~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~ 111 (116)
++|.++|.+|+.++...++.++..|..+++.
T Consensus 81 ~~p~~al~~a~~~l~~el~~l~~~f~~~~~~ 111 (117)
T KOG4392|consen 81 CSPADALTNAITDLIEELSLLENRFKAEAAL 111 (117)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999986
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=5.1e-39 Score=220.15 Aligned_cols=93 Identities=57% Similarity=0.903 Sum_probs=91.2
Q ss_pred CCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHH
Q 033562 13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIN 92 (116)
Q Consensus 13 ~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~ 92 (116)
|+|++||++..|++++|+++|+|.||||||||+||+.|+++|+|.||||+||||++++++|||||+++.+|.+||++|++
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 033562 93 DLDKELDTLKSAF 105 (116)
Q Consensus 93 ~l~~~~~~l~~~f 105 (116)
+|.+.|++++++|
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=2e-36 Score=200.87 Aligned_cols=77 Identities=47% Similarity=0.788 Sum_probs=72.7
Q ss_pred ceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (116)
Q Consensus 29 n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f 105 (116)
|+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+++++|.+||++|+++|.++|++++++|
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=6.9e-36 Score=201.78 Aligned_cols=82 Identities=32% Similarity=0.575 Sum_probs=79.4
Q ss_pred cCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 24 ~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
..+.+|+++|+|.||||||||+||+.|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|.+.|+++++
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 46889999999999999999999999999999999999999999999999999999899999999999999999999998
Q ss_pred HH
Q 033562 104 AF 105 (116)
Q Consensus 104 ~f 105 (116)
+|
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=8.9e-35 Score=196.36 Aligned_cols=79 Identities=29% Similarity=0.413 Sum_probs=76.3
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
.+.+|+++|+|.||||||||+||+.|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|.+.|++|++
T Consensus 7 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~~ 85 (85)
T PRK01146 7 EKEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD 85 (85)
T ss_pred ecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 5788999999999999999999999999999999999999999999999999999999999999999999999999863
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=1.8e-34 Score=194.13 Aligned_cols=79 Identities=30% Similarity=0.443 Sum_probs=75.7
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
.+..|+++|+|.||||||||+||++|+++|+|.||||++||||+++++|||||+++.+|.+||++|+++|++.|++|++
T Consensus 5 ~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~~ 83 (83)
T cd06927 5 EKEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFLD 83 (83)
T ss_pred EcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 3578999999999999999999999999999999999999999999999999999899999999999999999999863
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=2.8e-34 Score=193.14 Aligned_cols=78 Identities=40% Similarity=0.614 Sum_probs=74.9
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033562 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLK 102 (116)
Q Consensus 25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~ 102 (116)
++..|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+|.+||++|+++|.+.|++++
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 356799999999999999999999999999999999999999999999999999989999999999999999999985
No 8
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=1.2e-33 Score=195.80 Aligned_cols=97 Identities=36% Similarity=0.545 Sum_probs=91.1
Q ss_pred CeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHH
Q 033562 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLD 95 (116)
Q Consensus 16 ~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~ 95 (116)
.++.++....+..|+++|++.||||||||+|++.|+++++|+||||+||||+.+++++||||+++++|.+||++|++.++
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 45667777778999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 033562 96 KELDTLKSAFEAELAKHS 113 (116)
Q Consensus 96 ~~~~~l~~~f~~a~~~~~ 113 (116)
+.|++|.++| ++++++.
T Consensus 82 ~~~~~l~~~~-~~~e~~~ 98 (99)
T COG1761 82 KDLEELLDQF-EEFEKKE 98 (99)
T ss_pred HHHHHHHHHH-HHHHhhc
Confidence 9999999999 8887764
No 9
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=4.1e-34 Score=198.00 Aligned_cols=89 Identities=30% Similarity=0.585 Sum_probs=86.0
Q ss_pred CcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFE 106 (116)
Q Consensus 27 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~ 106 (116)
..++++|++.+|||||||.||++|+++|.|+||||+||||++++++|||||.++..++++|++|+++|.++|++++.+|+
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF~ 93 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKFE 93 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999999999999999999999999999998889999999999999999999999999
Q ss_pred HHHHhhhcc
Q 033562 107 AELAKHSRV 115 (116)
Q Consensus 107 ~a~~~~~~~ 115 (116)
+++++|+.+
T Consensus 94 ~~i~~~k~~ 102 (105)
T KOG3438|consen 94 EEIEEYKDQ 102 (105)
T ss_pred HHHHHhhhh
Confidence 999999754
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=99.93 E-value=5.9e-26 Score=152.82 Aligned_cols=76 Identities=39% Similarity=0.592 Sum_probs=72.0
Q ss_pred CCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCC------CceeEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q 033562 25 TKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRIHTTSQSSPMQAYNQAINDLDKEL 98 (116)
Q Consensus 25 ~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl------~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~ 98 (116)
.+..|+++|+|.||||||||+||+.|++ +.|.||||+||||+ .+++.|+|+|+|+.+|.+||++|++.|.+.|
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 3567999999999999999999999999 99999999999999 9999999999999999999999999999988
Q ss_pred HHH
Q 033562 99 DTL 101 (116)
Q Consensus 99 ~~l 101 (116)
+.|
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=2.1e-17 Score=105.89 Aligned_cols=65 Identities=35% Similarity=0.556 Sum_probs=61.0
Q ss_pred eEEEEecCCcchHHHHHHHhhcC-CCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033562 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (116)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~ 99 (116)
++|.+.|+|||+||+||..|+++ |+|.+++ ||..+++.++|+|+|+.+|.++|.+|++.|.+.|+
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 47999999999999999999999 9999999 99999999999999999999999999999998763
No 12
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=95.61 E-value=0.06 Score=41.43 Aligned_cols=51 Identities=14% Similarity=0.171 Sum_probs=41.1
Q ss_pred CCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 53 DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA 107 (116)
Q Consensus 53 ~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~ 107 (116)
.| |. |.|+..- .++..+.|.|+|+++|.+||..|++-|.+.++.|.+.+..
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 5554322 4999999999999999999999999999999998777643
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=95.44 E-value=0.03 Score=43.21 Aligned_cols=45 Identities=27% Similarity=0.240 Sum_probs=37.3
Q ss_pred CeeeeeecCCC------CCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033562 55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (116)
Q Consensus 55 ~V~fAgY~ipH------Pl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~ 99 (116)
=|.-+.|.|.- .-.+++.|-|.|+|.++|.+||..|++.|.+.+.
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 36677787643 3457899999999999999999999999988775
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=95.26 E-value=0.057 Score=41.81 Aligned_cols=52 Identities=17% Similarity=0.262 Sum_probs=43.8
Q ss_pred hcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 51 HRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 51 ~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
.+-.=|.-|+|++. |-.++..|.|-|+|..+|.+|+.+|++-|++.++.|.+
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 34445677888864 36799999999999999999999999999999998875
No 15
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=95.07 E-value=0.072 Score=43.13 Aligned_cols=49 Identities=24% Similarity=0.310 Sum_probs=40.8
Q ss_pred CeeeeeecCCC------CCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 55 NVLFAGYKLPH------PLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 55 ~V~fAgY~ipH------Pl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
-|.-+.|.|.. ...+++.+.|.|+|.++|.+||.+|++-|.+.+..|.+
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 23478999999999999999999999999999988865
No 16
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=94.93 E-value=0.059 Score=41.72 Aligned_cols=45 Identities=24% Similarity=0.313 Sum_probs=37.4
Q ss_pred eeeeeecCCCCC----------------CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q 033562 56 VLFAGYKLPHPL----------------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDT 100 (116)
Q Consensus 56 V~fAgY~ipHPl----------------~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~ 100 (116)
|..+.|.+.-|. .+++.|.|.|+|..+|.+||.+|++-|...++.
T Consensus 163 v~~v~~~~~~~~~~~~~~~~~~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~ 223 (224)
T smart00662 163 VDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 223 (224)
T ss_pred hhheeeeccCCccceecccchhhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence 555667766664 588999999999999999999999999887764
No 17
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=94.30 E-value=0.13 Score=41.93 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=40.7
Q ss_pred CeeeeeecCCCC------CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 55 NVLFAGYKLPHP------LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 55 ~V~fAgY~ipHP------l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
-|.-+.|.+.-. -.+++.+.|.|+|.++|.+||.+|++-|.+.+..|.+
T Consensus 171 PV~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~ 225 (310)
T PRK05182 171 PVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD 225 (310)
T ss_pred CccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 366677876542 1468999999999999999999999999999988765
No 18
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=94.11 E-value=0.064 Score=42.14 Aligned_cols=36 Identities=17% Similarity=0.172 Sum_probs=28.6
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN 55 (116)
Q Consensus 18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~ 55 (116)
++++.+. ..+.++|.+.|-|+||||.||-.|+.. |+
T Consensus 2 ~~~~~~~--~~~~~~f~~~g~~~t~~NalRRvlls~vp~ 38 (263)
T PRK00783 2 EIEILEL--DDRSARFVVEGVTPAFANAIRRAMIADVPT 38 (263)
T ss_pred ceEEEEc--CCcEEEEEEeCCCHHHHHHHHHHHHHcCCe
Confidence 3555543 347899999999999999999999985 54
No 19
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=94.10 E-value=0.13 Score=42.39 Aligned_cols=49 Identities=18% Similarity=0.169 Sum_probs=41.2
Q ss_pred CeeeeeecCCCC-----CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 55 NVLFAGYKLPHP-----LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 55 ~V~fAgY~ipHP-----l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
=|.-+.|.|..- ..+++.+-|.|+|.++|.+||..|++-|.+.+.-+.+
T Consensus 170 PV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~ 223 (327)
T CHL00013 170 PVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH 223 (327)
T ss_pred CeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 366777887651 2578999999999999999999999999999887764
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=93.03 E-value=0.13 Score=40.33 Aligned_cols=36 Identities=14% Similarity=0.149 Sum_probs=28.9
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CC
Q 033562 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-EN 55 (116)
Q Consensus 18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~ 55 (116)
++++.+. .++.+.|.+.|-|+|+||.||-.|+.. |+
T Consensus 2 ~~~~~~~--~~~~~~f~~~g~~~s~~NalRRills~vp~ 38 (259)
T cd07030 2 EIEVLEL--DDDRARFVLEGVPPAFANAIRRAIISEVPT 38 (259)
T ss_pred ceEEEec--CCCEEEEEEeCCCHHHHHHHHHHHHhcCCe
Confidence 4555543 358899999999999999999999884 54
No 21
>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=93.02 E-value=0.21 Score=39.85 Aligned_cols=53 Identities=17% Similarity=0.140 Sum_probs=43.8
Q ss_pred CeeeeeecCCCCC-----------CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 55 NVLFAGYKLPHPL-----------QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA 107 (116)
Q Consensus 55 ~V~fAgY~ipHPl-----------~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~ 107 (116)
...||-..+.||- .+.+.+.|-|.|..+|.++|.+|++-|.+.++.|.+.+..
T Consensus 201 ~c~~c~~c~~~~~~~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~ 264 (265)
T cd07031 201 WPKSENACIEEPPEKDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264 (265)
T ss_pred cCchhHHHhhcccccCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3455555566653 5789999999999999999999999999999999988653
No 22
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=91.93 E-value=0.31 Score=40.20 Aligned_cols=47 Identities=26% Similarity=0.262 Sum_probs=36.8
Q ss_pred eEeeccCCCcceeEEEE----ecCCcchHHHHHHHhhc-CCCeeeeeecCCC
Q 033562 19 VSYERDTKIINAASFTI----EREEHTIGNILRMQLHR-DENVLFAGYKLPH 65 (116)
Q Consensus 19 v~~~~~~k~~n~~~~~i----~~EDHTLgNlLr~~L~~-~~~V~fAgY~ipH 65 (116)
+....+....+.+.|.| .|..|||||+||-.|+. .|+.-+.+-+|.+
T Consensus 10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 44455556678899999 67889999999999998 4887777777654
No 23
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=91.79 E-value=0.38 Score=39.20 Aligned_cols=47 Identities=26% Similarity=0.311 Sum_probs=34.8
Q ss_pred eeEeeccCCCcceeEEEEe----cCCcchHHHHHHHhhcC-CCeeeeeecCC
Q 033562 18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKLP 64 (116)
Q Consensus 18 Kv~~~~~~k~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAgY~ip 64 (116)
++++...+...+.+.|.+. |.++|+||+||-.|+.. |+.-..+-+|.
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 3444433334689999996 99999999999999984 77666666654
No 24
>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=91.14 E-value=0.32 Score=37.53 Aligned_cols=39 Identities=28% Similarity=0.336 Sum_probs=30.7
Q ss_pred CCcceeEEEE----ecCCcchHHHHHHHhhcC-CCeeeeeecCC
Q 033562 26 KIINAASFTI----EREEHTIGNILRMQLHRD-ENVLFAGYKLP 64 (116)
Q Consensus 26 k~~n~~~~~i----~~EDHTLgNlLr~~L~~~-~~V~fAgY~ip 64 (116)
...+.+.|.| .|.++|+||.||-.|+.. |+.-.-+-+|.
T Consensus 6 ~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~ 49 (215)
T cd06928 6 KRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE 49 (215)
T ss_pred CCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEc
Confidence 3468899999 779999999999999884 77665555553
No 25
>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=91.04 E-value=0.26 Score=38.19 Aligned_cols=31 Identities=13% Similarity=0.216 Sum_probs=27.0
Q ss_pred CCcceeEEEEecCCcchHHHHHHHhhcC-CCe
Q 033562 26 KIINAASFTIEREEHTIGNILRMQLHRD-ENV 56 (116)
Q Consensus 26 k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V 56 (116)
+.++.+.|.+.|-|+|+||+||-.|+.. |+.
T Consensus 8 ~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~ 39 (212)
T cd07028 8 ADKDNVDFILSGVDLAMANALRRVMIAEVPTM 39 (212)
T ss_pred cCCCEEEEEEEccChhHHHHHHHHHHHcCcce
Confidence 5678899999999999999999999985 553
No 26
>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=90.20 E-value=0.63 Score=37.09 Aligned_cols=39 Identities=15% Similarity=0.260 Sum_probs=30.0
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC-CCeee
Q 033562 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLF 58 (116)
Q Consensus 18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~f 58 (116)
+|++.+. .++.++|.+.+=|+|+||+||-.|+.. |..-.
T Consensus 2 ~i~i~~~--~~~~~~F~l~~~~~s~aNALRRillsevPt~AI 41 (265)
T cd07031 2 RVEITEL--TDDKVKFILENTDLSVANSLRRVMIAEVPTLAI 41 (265)
T ss_pred cEEEEEc--CCCEEEEEEEcCcHHHHHHHHHHHHHcCccceE
Confidence 3555543 458899999999999999999999884 65433
No 27
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=89.86 E-value=0.6 Score=35.93 Aligned_cols=37 Identities=14% Similarity=0.222 Sum_probs=29.8
Q ss_pred ccCCCcceeEEEEecCCcchHHHHHHHhhcC-CCeeeee
Q 033562 23 RDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVLFAG 60 (116)
Q Consensus 23 ~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAg 60 (116)
.-++..+.++|.+. -|.|+||.||-.|+.. |+.-.-+
T Consensus 8 ~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~ 45 (195)
T PRK14979 8 EKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN 45 (195)
T ss_pred eeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence 33678889999999 9999999999999884 6644444
No 28
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=89.81 E-value=0.44 Score=36.84 Aligned_cols=33 Identities=24% Similarity=0.299 Sum_probs=26.4
Q ss_pred eEEEEecCCcchHHHHHHHhhcC-CCeeeeeecC
Q 033562 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKL 63 (116)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~i 63 (116)
+.|++.+-++|+||+||-.|+.. |+.-.-+.+|
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 6655554444
No 29
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=89.24 E-value=0.8 Score=37.58 Aligned_cols=45 Identities=18% Similarity=0.017 Sum_probs=31.8
Q ss_pred eEeeccC--CCcceeEEEEecCCcchHHHHHHHhhc-CCCeeeeeecC
Q 033562 19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHR-DENVLFAGYKL 63 (116)
Q Consensus 19 v~~~~~~--k~~n~~~~~i~~EDHTLgNlLr~~L~~-~~~V~fAgY~i 63 (116)
|++...+ ...-.++|...|-+|||||+||-.|+. .|+.-.-+-+|
T Consensus 7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I 54 (317)
T COG0202 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEI 54 (317)
T ss_pred eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEE
Confidence 4444333 336688999999999999999999988 47644433333
No 30
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=89.07 E-value=1.2 Score=34.98 Aligned_cols=41 Identities=20% Similarity=0.231 Sum_probs=37.0
Q ss_pred CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA 107 (116)
Q Consensus 67 l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~ 107 (116)
..++..+.+.|.|..+|.+++..|++-|...++.|.++++.
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 36778899999999999999999999999999999988764
No 31
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=86.59 E-value=1.8 Score=33.87 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=33.2
Q ss_pred CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033562 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (116)
Q Consensus 68 ~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~ 104 (116)
.+...+.|.|.|..+|.++|+.|++-|.+.++.|.++
T Consensus 222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~ 258 (259)
T cd07030 222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258 (259)
T ss_pred CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4567888999999999999999999999999998765
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=83.91 E-value=3 Score=33.93 Aligned_cols=37 Identities=22% Similarity=0.266 Sum_probs=33.8
Q ss_pred CCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 67 LQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 67 l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
-.+.+.+.|-|.|...|.+.+.+|++-|.+.|+.+++
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 4677999999999999999999999999999998875
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=81.82 E-value=1.7 Score=35.22 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=23.6
Q ss_pred ecCCcchHHHHHHHhhcC-CCeeeeeecCC
Q 033562 36 EREEHTIGNILRMQLHRD-ENVLFAGYKLP 64 (116)
Q Consensus 36 ~~EDHTLgNlLr~~L~~~-~~V~fAgY~ip 64 (116)
.|..|||||+||-.|+.. |++-..+-+|.
T Consensus 11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~ 40 (297)
T TIGR02027 11 RGFGITLGNALRRVLLSSIPGAAITAVKID 40 (297)
T ss_pred CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence 688999999999999984 87776666654
No 34
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=80.34 E-value=1.4 Score=36.83 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=21.8
Q ss_pred CCcchHHHHHHHhhcCCCeeeeee
Q 033562 38 EEHTIGNILRMQLHRDENVLFAGY 61 (116)
Q Consensus 38 EDHTLgNlLr~~L~~~~~V~fAgY 61 (116)
..|++.|.||..|.+||+|.+.|=
T Consensus 183 dT~sF~~aLraALReDPDVIlvGE 206 (353)
T COG2805 183 DTLSFANALRAALREDPDVILVGE 206 (353)
T ss_pred cHHHHHHHHHHHhhcCCCEEEEec
Confidence 349999999999999999999993
No 35
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=67.16 E-value=6.8 Score=28.06 Aligned_cols=38 Identities=16% Similarity=0.121 Sum_probs=29.5
Q ss_pred CcceeEEEEecCCcchHHHHHHHhhcCCC--eeeeeecCC
Q 033562 27 IINAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLP 64 (116)
Q Consensus 27 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~ip 64 (116)
.+..+..++.+|.|++|..+-..+++..+ |.+-|..+|
T Consensus 3 ~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp 42 (137)
T PRK02261 3 KKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTS 42 (137)
T ss_pred CCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCC
Confidence 34457788999999999999999999866 555555554
No 36
>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=62.77 E-value=21 Score=24.00 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=25.0
Q ss_pred eEEEEecCCcchHHHHHHHhhcCCC--eeeeeecCC
Q 033562 31 ASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLP 64 (116)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~ip 64 (116)
+..++.+|.|++|..+-..+++..+ |.+.|-.+|
T Consensus 3 l~~~~~~e~H~lG~~~~~~~l~~~G~~V~~lg~~~~ 38 (119)
T cd02067 3 VIATVGGDGHDIGKNIVARALRDAGFEVIDLGVDVP 38 (119)
T ss_pred EEEeeCCchhhHHHHHHHHHHHHCCCEEEECCCCCC
Confidence 4567899999999999999998766 334443333
No 37
>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=62.00 E-value=19 Score=27.00 Aligned_cols=39 Identities=23% Similarity=0.254 Sum_probs=29.9
Q ss_pred cceeEEEEecCCcchHHHHHHHhhcCCC--eeeeeecCCCC
Q 033562 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (116)
Q Consensus 28 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~ipHP 66 (116)
+..+..++.||-|+||-.+-..+++..+ |.+.|-.+|+.
T Consensus 83 ~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~ 123 (201)
T cd02070 83 GKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPE 123 (201)
T ss_pred CeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHH
Confidence 3457788899999999888888888765 55667666654
No 38
>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=61.05 E-value=20 Score=26.88 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=31.2
Q ss_pred cceeEEEEecCCcchHHHHHHHhhcCCC--eeeeeecCCCC
Q 033562 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (116)
Q Consensus 28 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~ipHP 66 (116)
...+-.++.||.|+||-.+...+++..+ |.+.|-.+|-.
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e 125 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPID 125 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHH
Confidence 3457888899999999999999999865 66677666643
No 39
>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=60.10 E-value=26 Score=24.02 Aligned_cols=26 Identities=15% Similarity=0.088 Sum_probs=22.7
Q ss_pred eEEEEecCCcchHHHHHHHhhcCCCe
Q 033562 31 ASFTIEREEHTIGNILRMQLHRDENV 56 (116)
Q Consensus 31 ~~~~i~~EDHTLgNlLr~~L~~~~~V 56 (116)
+.+++.+|.|++|..+-..+++..+.
T Consensus 3 v~~~~~gd~H~lG~~~~~~~l~~~G~ 28 (122)
T cd02071 3 LVAKPGLDGHDRGAKVIARALRDAGF 28 (122)
T ss_pred EEEecCCChhHHHHHHHHHHHHHCCC
Confidence 56788999999999999999998763
No 40
>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=58.75 E-value=22 Score=27.28 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=31.0
Q ss_pred cceeEEEEecCCcchHHHHHHHhhcCCC--eeeeeecCCCC
Q 033562 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (116)
Q Consensus 28 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~ipHP 66 (116)
...+..++.||.|.||-.+...+++..+ |.+-|-++|-+
T Consensus 89 ~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e 129 (213)
T cd02069 89 GKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIE 129 (213)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHH
Confidence 3457788899999999999999999866 66777666643
No 41
>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=57.06 E-value=46 Score=20.84 Aligned_cols=68 Identities=13% Similarity=0.164 Sum_probs=36.5
Q ss_pred eeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCC-CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q 033562 30 AASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL-QYKIIVRIHTTSQSSPMQAYNQAINDLDKELD 99 (116)
Q Consensus 30 ~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl-~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~ 99 (116)
++.|++.++-=+|..+|...-..+=++.-. -..|++- .....++|++++..+ .+.++++++.|...+.
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 345555544334444444333333333222 2334432 456889999987533 4777888877776544
No 42
>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=55.63 E-value=50 Score=21.66 Aligned_cols=34 Identities=18% Similarity=0.281 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033562 79 SQSSPMQAYNQAINDLDKELDTLKSAFEAELAKH 112 (116)
Q Consensus 79 ~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~~ 112 (116)
++.+|.++|..-+..|.+.+.+++-.+..--..|
T Consensus 7 ~s~~p~~~Ls~vl~~LqDE~~hm~~e~~~L~~~~ 40 (79)
T PF06657_consen 7 PSQSPGEALSEVLKALQDEFGHMKMEHQELQDEY 40 (79)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999999998887764444
No 43
>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=47.95 E-value=62 Score=22.23 Aligned_cols=71 Identities=17% Similarity=0.232 Sum_probs=41.6
Q ss_pred cccceeeCCCCeeeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcCCCeeeee----e----------cCCCCCCcee
Q 033562 6 RYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG----Y----------KLPHPLQYKI 71 (116)
Q Consensus 6 ~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAg----Y----------~ipHPl~~~i 71 (116)
-.+++.+|.|.+.|.+.......|.+-+.-.. ++-+.|-= +.+.....+.+|| | .++.|+...+
T Consensus 16 Y~~v~~IP~GA~nI~I~e~~~s~n~Lalk~~~-g~y~lNg~-~~i~~~~~~~~aGt~~~Y~~~~~~~E~i~~~GPl~e~l 93 (114)
T PF05986_consen 16 YNKVVTIPAGARNIRITERRPSSNYLALKNSD-GKYVLNGN-WVISWPGTYSVAGTTFEYSRSDDNLERITAPGPLTEDL 93 (114)
T ss_pred ceEEEECCCCceEEEEEEeecCccEEEEEecC-CcEEEcCC-ccccCCcCEEeCCeEEEEEecCCCCEEEEcCCCCCCCE
Confidence 35889999999999999865555555444333 45544442 2222233355555 2 3456776666
Q ss_pred EEEEEeC
Q 033562 72 IVRIHTT 78 (116)
Q Consensus 72 ~lrIqt~ 78 (116)
.|-|-..
T Consensus 94 ~v~vl~~ 100 (114)
T PF05986_consen 94 IVQVLSQ 100 (114)
T ss_pred EEEEEEe
Confidence 6655433
No 44
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=45.72 E-value=1e+02 Score=23.44 Aligned_cols=34 Identities=12% Similarity=0.133 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 033562 82 SPMQAYNQAINDLDKELDTLKSAFEAELAKHSRV 115 (116)
Q Consensus 82 ~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~~~~~ 115 (116)
.....+.+++....+..+++.+.....++.|++.
T Consensus 124 ~ir~~I~~~i~~~~~~~~eid~~Vr~ki~~y~r~ 157 (183)
T PF04368_consen 124 RIRNIIFKSIEEYLKEEEEIDDEVREKIKSYKRK 157 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcC
Confidence 4568899999999999999999999999999763
No 45
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=45.69 E-value=47 Score=27.01 Aligned_cols=77 Identities=18% Similarity=0.130 Sum_probs=56.7
Q ss_pred eeEEEE-ecCCcchHHHHHHHhh--------cCCCeeeeeecCCCCC---------CceeEEEEEeCCCCCHHHHHHHHH
Q 033562 30 AASFTI-EREEHTIGNILRMQLH--------RDENVLFAGYKLPHPL---------QYKIIVRIHTTSQSSPMQAYNQAI 91 (116)
Q Consensus 30 ~~~~~i-~~EDHTLgNlLr~~L~--------~~~~V~fAgY~ipHPl---------~~~i~lrIqt~~~~~p~e~l~~a~ 91 (116)
.+.+.| ++=| |.||+.+. +-|.+..+++.-+-|- -+++++.|...|+..|..++..|+
T Consensus 176 ta~V~FeYDPd----n~lrhT~y~~e~~~~~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi 251 (285)
T KOG1522|consen 176 TAAVAFEYDPD----NKLRHTLYWFEEDDLIEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGI 251 (285)
T ss_pred cceEEEEECcc----HhhhccCCCccccchhhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHH
Confidence 455555 3334 77777665 3466777777765111 278999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 033562 92 NDLDKELDTLKSAFEAELA 110 (116)
Q Consensus 92 ~~l~~~~~~l~~~f~~a~~ 110 (116)
+-|.+.++.|.-......+
T Consensus 252 ~iLk~Kl~~l~~~l~~~~q 270 (285)
T KOG1522|consen 252 DILKEKLAALRLALSTEDQ 270 (285)
T ss_pred HHHHHHHHHHHhhhcccch
Confidence 9999999999887765544
No 46
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=45.59 E-value=41 Score=27.65 Aligned_cols=40 Identities=15% Similarity=0.081 Sum_probs=35.7
Q ss_pred CceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 68 QYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEA 107 (116)
Q Consensus 68 ~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~ 107 (116)
.++..+.+-|++.+.|.+|+..|.+-+.+.|+.+.+.+..
T Consensus 187 ~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~ 226 (317)
T COG0202 187 KDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPK 226 (317)
T ss_pred ceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3778888999999999999999999999999999888764
No 47
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=41.15 E-value=1.2e+02 Score=21.11 Aligned_cols=43 Identities=21% Similarity=0.342 Sum_probs=31.1
Q ss_pred CCCceeEEEEEeCCC--------CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 66 PLQYKIIVRIHTTSQ--------SSPMQAYNQAINDLDKELDTLKSAFEAE 108 (116)
Q Consensus 66 Pl~~~i~lrIqt~~~--------~~p~e~l~~a~~~l~~~~~~l~~~f~~a 108 (116)
+....+.++|..+++ .++..|+..|++.|..++.-.+++.++.
T Consensus 47 ~~~~~ve~ti~~~~g~l~a~~~~~d~YaAID~a~dKLerqlrK~K~K~~~~ 97 (110)
T COG1544 47 RSRFKVEATIHLPGGILRAEAEHEDMYAAIDLAIDKLERQLRKHKEKLKDH 97 (110)
T ss_pred ccceEEEEEEEcCCceEEEeecCCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 344555555555543 3899999999999998888888877654
No 48
>COG1027 AspA Aspartate ammonia-lyase [Amino acid transport and metabolism]
Probab=40.85 E-value=60 Score=28.21 Aligned_cols=67 Identities=22% Similarity=0.291 Sum_probs=46.6
Q ss_pred hHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 033562 42 IGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSP---MQAYNQAINDLDKELDTLKSAFEAELAKHSR 114 (116)
Q Consensus 42 LgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p---~e~l~~a~~~l~~~~~~l~~~f~~a~~~~~~ 114 (116)
++|.=-+.|-..++ -|.+-||.++ +++.=-|+ ++-| .=++-.++..|.+.++.|.+.|++..++|+.
T Consensus 112 IAN~AlE~lG~~KG----eY~~~hPndh-VNmsQSTN-D~yPTa~ria~~~~l~~L~~al~~L~~af~~Ka~EF~~ 181 (471)
T COG1027 112 IANRALELLGHEKG----EYQYLHPNDH-VNMSQSTN-DAYPTAFRIAVYKSLRKLIDALEDLIEAFERKAKEFAD 181 (471)
T ss_pred HHHHHHHHhcCCCC----ceeeeCCccc-cchhhccc-ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 55555555544443 3999999875 34443333 3333 3567788889999999999999999999875
No 49
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.44 E-value=79 Score=25.74 Aligned_cols=51 Identities=18% Similarity=0.212 Sum_probs=38.8
Q ss_pred chHHHHHHHhhc-CCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHH
Q 033562 41 TIGNILRMQLHR-DENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAI 91 (116)
Q Consensus 41 TLgNlLr~~L~~-~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~ 91 (116)
++-|.|+...-+ -+.|+|+-|.+-||.-=-+.+..-|+..-....+++.++
T Consensus 93 ~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~ 144 (276)
T KOG2972|consen 93 GIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIF 144 (276)
T ss_pred HHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHH
Confidence 678889888886 488999999999999988888888875433333344433
No 50
>PHA02766 hypothetical protein; Provisional
Probab=39.38 E-value=27 Score=22.43 Aligned_cols=50 Identities=24% Similarity=0.382 Sum_probs=32.3
Q ss_pred eeEEEEecCCcchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHH
Q 033562 30 AASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAI 91 (116)
Q Consensus 30 ~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~ 91 (116)
.+.|+|..||..- ++.-. |+.+ --||.+++.++|.|+.-.+-.+||.--+
T Consensus 16 kisfeineedyqq--liela--------fsqf--iyplndnieikintkeladnekallyei 65 (73)
T PHA02766 16 KISFEINEEDYQQ--LIELA--------FSQF--IYPLNDNIEIKINTKELADNEKALLYEI 65 (73)
T ss_pred EEEEEECHHHHHH--HHHHH--------HHhh--eeeCCCceEEEechHhhccchhhHhHhh
Confidence 5788888888542 22111 2212 3489999999999987666666665444
No 51
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=39.31 E-value=26 Score=30.82 Aligned_cols=26 Identities=27% Similarity=0.395 Sum_probs=23.5
Q ss_pred ecCCcchHHHHHHHhhcCCCeeeeee
Q 033562 36 EREEHTIGNILRMQLHRDENVLFAGY 61 (116)
Q Consensus 36 ~~EDHTLgNlLr~~L~~~~~V~fAgY 61 (116)
.+-+=|+.+.||..|.+||+|.+.|=
T Consensus 310 ~k~gltfa~~LRa~LRqDPDvImVGE 335 (500)
T COG2804 310 PKIGLTFARALRAILRQDPDVIMVGE 335 (500)
T ss_pred cccCCCHHHHHHHHhccCCCeEEEec
Confidence 46688999999999999999999993
No 52
>PRK00549 competence damage-inducible protein A; Provisional
Probab=38.88 E-value=1.4e+02 Score=25.07 Aligned_cols=37 Identities=16% Similarity=0.321 Sum_probs=27.0
Q ss_pred cchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCC
Q 033562 40 HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQ 80 (116)
Q Consensus 40 HTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~ 80 (116)
=+|...|...+...++|.++.| || ...+.+|+..++.
T Consensus 191 s~l~~~L~~l~~~~~~v~ig~~--~~--~~~~~vrl~~~~~ 227 (414)
T PRK00549 191 SQLATTLRDLIDNQTNPTIAPY--AK--DGEVTLRLTAKAR 227 (414)
T ss_pred HHHHHHHHHHHhcCCCCEEEEC--cc--CCEEEEEEEEecC
Confidence 4677888888778899998766 33 3667888887653
No 53
>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=38.31 E-value=50 Score=26.86 Aligned_cols=34 Identities=18% Similarity=0.174 Sum_probs=27.7
Q ss_pred eeEeeccCCCcceeEEEEecCCcchHHHHHHHhhcC
Q 033562 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (116)
Q Consensus 18 Kv~~~~~~k~~n~~~~~i~~EDHTLgNlLr~~L~~~ 53 (116)
||++.+ ..++.++|.+.|-|=++.|+||-.|+..
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 455554 3558899999999999999999998874
No 54
>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=36.28 E-value=1.1e+02 Score=23.45 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=26.0
Q ss_pred CcceeEEEEecCCcchHHHHHHHhhcCCCeeeee
Q 033562 27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60 (116)
Q Consensus 27 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAg 60 (116)
.++...+.-....+++..+|+..|..+|++.+.|
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 3455665555688999999999999999998887
No 55
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=35.22 E-value=60 Score=23.55 Aligned_cols=18 Identities=50% Similarity=0.737 Sum_probs=10.4
Q ss_pred hhcCCCeeeeeecCCCCCC
Q 033562 50 LHRDENVLFAGYKLPHPLQ 68 (116)
Q Consensus 50 L~~~~~V~fAgY~ipHPl~ 68 (116)
|++.-+..+.||+ ||||.
T Consensus 9 ~~~~~~~~~~~~~-~~~~~ 26 (127)
T PRK12729 9 LWRIYNSGYSGNK-PHPLS 26 (127)
T ss_pred HHHHHhcccCCCC-CCCCC
Confidence 3444444455554 99984
No 56
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=32.66 E-value=2.2e+02 Score=21.84 Aligned_cols=80 Identities=23% Similarity=0.238 Sum_probs=55.1
Q ss_pred EecCCcchHHHHHHHhhcCCCeeeee---------------------------ecCCCCCCceeEEEEEeCCCCCHHHH-
Q 033562 35 IEREEHTIGNILRMQLHRDENVLFAG---------------------------YKLPHPLQYKIIVRIHTTSQSSPMQA- 86 (116)
Q Consensus 35 i~~EDHTLgNlLr~~L~~~~~V~fAg---------------------------Y~ipHPl~~~i~lrIqt~~~~~p~e~- 86 (116)
..+|||-=.|-|-++|-++-+|.-|- |.-.-|.-+.+..-|..+-.-+|.+|
T Consensus 71 ~q~~d~Y~~nGlL~mLdRNrrvK~aPe~wq~~~~~fd~ViTCEERcfdaicEdly~rg~~ln~~v~~iNvDIkD~~e~A~ 150 (197)
T COG5211 71 MQNEDHYRENGLLYMLDRNRRVKEAPENWQQRSEDFDLVITCEERCFDAICEDLYARGPSLNQCVFMINVDIKDTPEDAI 150 (197)
T ss_pred hhhhhhhhhccHHHHHHhcchhhhCchhhhhccccccEEEEehHHHHHHHHHHHHhcCccccccEEEEEeeccCChhhhh
Confidence 35788888888888888887766543 44455667777777776544355544
Q ss_pred -----HHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 033562 87 -----YNQAINDLDKELDTLKSAFEAELAKHSR 114 (116)
Q Consensus 87 -----l~~a~~~l~~~~~~l~~~f~~a~~~~~~ 114 (116)
+.+-++-|-+.-+.|+..|.+.+.+|++
T Consensus 151 ~G~kaILelvd~L~~~~e~lE~~~~sil~~~qs 183 (197)
T COG5211 151 AGAKAILELVDVLAKEEERLEYAVDSILRRYQS 183 (197)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4444566667777788888888888875
No 57
>PHA02781 hypothetical protein; Provisional
Probab=30.25 E-value=43 Score=21.80 Aligned_cols=26 Identities=31% Similarity=0.362 Sum_probs=20.1
Q ss_pred eeeEeeccCCCcceeEEEEecCCcch
Q 033562 17 KKVSYERDTKIINAASFTIEREEHTI 42 (116)
Q Consensus 17 ~Kv~~~~~~k~~n~~~~~i~~EDHTL 42 (116)
.|+++..|+|+.|.+++...-|--|+
T Consensus 6 dkikitvdskignvvtisynlekiti 31 (78)
T PHA02781 6 DKIKITVDSKIGNVVTISYNLEKITI 31 (78)
T ss_pred ceEEEEeecccCcEEEEEeeeEEEEE
Confidence 47888889999998888876665554
No 58
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=30.20 E-value=1.3e+02 Score=17.99 Aligned_cols=29 Identities=14% Similarity=0.281 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033562 83 PMQAYNQAINDLDKELDTLKSAFEAELAK 111 (116)
Q Consensus 83 p~e~l~~a~~~l~~~~~~l~~~f~~a~~~ 111 (116)
+-.+|-..+..+.+.+.++++.+...+++
T Consensus 2 ~~~~l~~ql~~l~~~l~elk~~l~~Q~kE 30 (45)
T PF11598_consen 2 VDSQLIKQLSELNQMLQELKELLRQQIKE 30 (45)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567788888888888888888877765
No 59
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=30.13 E-value=1.2e+02 Score=27.17 Aligned_cols=52 Identities=17% Similarity=0.256 Sum_probs=40.4
Q ss_pred ecCCCCCC------------ceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033562 61 YKLPHPLQ------------YKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAELAKH 112 (116)
Q Consensus 61 Y~ipHPl~------------~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~~ 112 (116)
|.+||=+. ++...-++-++-++.+-||++++..+..+.+.++..++++-+..
T Consensus 583 ~~~p~~l~~e~eki~~ee~r~~~~~vleekslvdtvyalkd~v~~lqqd~~kmkk~leeEqkaR 646 (661)
T KOG2070|consen 583 YSQPQVLLPEEEKILMEETRSNGQSVLEEKSLVDTVYALKDEVSELQQDNKKMKKVLEEEQKAR 646 (661)
T ss_pred cccceehhhhHHHHHHHhcccccceeecccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777652 34555566666678889999999999999999999998876643
No 60
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=29.81 E-value=1.1e+02 Score=23.37 Aligned_cols=30 Identities=23% Similarity=0.422 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 033562 85 QAYNQAINDLDKELDTLKSAFEAELAKHSR 114 (116)
Q Consensus 85 e~l~~a~~~l~~~~~~l~~~f~~a~~~~~~ 114 (116)
++|...+..+....++|...|..++.+.+.
T Consensus 110 evL~qr~~kle~ErdeL~~kf~~~i~evqQ 139 (201)
T PF13851_consen 110 EVLEQRFEKLEQERDELYRKFESAIQEVQQ 139 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678888999999999999999999987754
No 61
>COG4495 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.18 E-value=1e+02 Score=21.84 Aligned_cols=50 Identities=18% Similarity=0.192 Sum_probs=31.3
Q ss_pred eeeeec-CCCCCC---ceeEEEEEeCCCCCHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Q 033562 57 LFAGYK-LPHPLQ---YKIIVRIHTTSQSSPMQAYNQAINDLDK--ELDTLKSAFEAEL 109 (116)
Q Consensus 57 ~fAgY~-ipHPl~---~~i~lrIqt~~~~~p~e~l~~a~~~l~~--~~~~l~~~f~~a~ 109 (116)
.+++|+ +|||-- +.-...++.+ +..+++.+|.++=.+ ..++|.+.|++.+
T Consensus 38 ~~fDY~a~~yP~G~~~~d~v~yFn~e---~I~eVv~~Gy~D~~e~~~~eqL~qa~~~~~ 93 (109)
T COG4495 38 TMFDYSACPYPEGELSDDKVAYFNHE---NIDEVVFEGYEDDDEALRFEQLKQAKKEYL 93 (109)
T ss_pred eeeccccccCCccccccceEEEeccc---chHHHHhhhcccchHHHHHHHHHHHHhhhc
Confidence 478888 799975 3444444433 678999988876554 3445555554433
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=27.79 E-value=1.6e+02 Score=24.31 Aligned_cols=51 Identities=8% Similarity=0.132 Sum_probs=40.8
Q ss_pred cchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHH
Q 033562 40 HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIND 93 (116)
Q Consensus 40 HTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~ 93 (116)
|| |-.+...|=... +.=.+.+||.|+-+-..+.+++++.++. +-+.++++.
T Consensus 190 ~~-a~av~~VlP~L~-i~g~AvrVPt~~vs~~dl~v~l~~~~t~-eeV~~~l~~ 240 (333)
T TIGR01546 190 HH-GPDVQTVIPNLN-IETMAFVVPTTLMHVHSIMVELKKPVTK-DDIIDILEN 240 (333)
T ss_pred ch-HHHHHHcCCCCC-ccEEEEEeCCCCcEEEEEEEEECCCCCH-HHHHHHHHh
Confidence 77 888888887766 7888899999999999999999887654 445555554
No 63
>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=27.10 E-value=1.7e+02 Score=18.63 Aligned_cols=33 Identities=24% Similarity=0.387 Sum_probs=23.9
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (116)
Q Consensus 72 ~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f 105 (116)
.+++...+ .+...|+..|++.|...+...++..
T Consensus 60 ~l~a~~~~-~d~~~Aid~a~~klerql~k~k~k~ 92 (95)
T TIGR00741 60 VIRASAEH-EDMYAAIDLAIDKLERQLRKLKEKR 92 (95)
T ss_pred EEEEEEec-CcHHHHHHHHHHHHHHHHHHHHhhh
Confidence 34444443 4899999999998888887777654
No 64
>cd00330 phosphagen_kinases Phosphagen (guanidino) kinases. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) a
Probab=27.04 E-value=3.1e+02 Score=21.54 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=11.8
Q ss_pred EEEEe-CCCCCHHHHHHHHH
Q 033562 73 VRIHT-TSQSSPMQAYNQAI 91 (116)
Q Consensus 73 lrIqt-~~~~~p~e~l~~a~ 91 (116)
||||+ ..|.+..+|++++.
T Consensus 109 LrI~s~~~G~~l~~~~~r~~ 128 (236)
T cd00330 109 LRIISMQKGGQLKEVMKRAN 128 (236)
T ss_pred EEEEEEcCCCCHHHHHHHHH
Confidence 45666 33457777777665
No 65
>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=26.79 E-value=1.9e+02 Score=22.62 Aligned_cols=32 Identities=19% Similarity=0.367 Sum_probs=24.4
Q ss_pred ceeEEEEecC-CcchHHHHHHHhhcCCCeeeee
Q 033562 29 NAASFTIERE-EHTIGNILRMQLHRDENVLFAG 60 (116)
Q Consensus 29 n~~~~~i~~E-DHTLgNlLr~~L~~~~~V~fAg 60 (116)
+..-+.+..+ +-|+..+|+..|..+|+|.+.|
T Consensus 124 ~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vg 156 (264)
T cd01129 124 GINQVQVNEKAGLTFARGLRAILRQDPDIIMVG 156 (264)
T ss_pred CceEEEeCCcCCcCHHHHHHHHhccCCCEEEec
Confidence 3334444433 4699999999999999999888
No 66
>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=26.77 E-value=1.5e+02 Score=25.87 Aligned_cols=30 Identities=20% Similarity=0.363 Sum_probs=23.7
Q ss_pred eEEEEec-CCcchHHHHHHHhhcCCCeeeee
Q 033562 31 ASFTIER-EEHTIGNILRMQLHRDENVLFAG 60 (116)
Q Consensus 31 ~~~~i~~-EDHTLgNlLr~~L~~~~~V~fAg 60 (116)
.-+.+.. ...|+.++|+..|.++|+|.+.|
T Consensus 362 ~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vG 392 (564)
T TIGR02538 362 NQVNVNPKIGLTFAAALRSFLRQDPDIIMVG 392 (564)
T ss_pred eEEEeccccCCCHHHHHHHHhccCCCEEEeC
Confidence 3444432 24799999999999999999988
No 67
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=26.68 E-value=3.4e+02 Score=21.76 Aligned_cols=71 Identities=11% Similarity=0.123 Sum_probs=42.2
Q ss_pred eeEEEEecCC-cchHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033562 30 AASFTIEREE-HTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKS 103 (116)
Q Consensus 30 ~~~~~i~~ED-HTLgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~ 103 (116)
+-++.+.|-. =.|+-.|+......|+|.++.|--....... .|.|+.+. .-.++++.+++.+...+.....
T Consensus 180 ~~~~~~~gi~ES~la~~L~~i~~~~~~~~i~s~p~~~~~~~~-~~~i~~~~--~~~~~~~~~~~~~~~~i~~~~~ 251 (255)
T COG1058 180 SRVLRVFGIGESSLAPTLKDLQDEQPNVTIASYPKDGEVRLR-ELVIRAEA--RDEEEADALLRWLEGRLRARGA 251 (255)
T ss_pred EEEEEEcCCChHHHHHHHHHHHhcCCCCEEEecCCCCceecc-ceEEEEec--CCHHHHHHHHHHHHHHHHHhhh
Confidence 3345554333 3588888888888999988877544433221 33355543 2356666666666665554443
No 68
>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=26.64 E-value=46 Score=19.63 Aligned_cols=23 Identities=17% Similarity=0.081 Sum_probs=9.6
Q ss_pred eEeeccCCCcceeEEEEecCCcch
Q 033562 19 VSYERDTKIINAASFTIEREEHTI 42 (116)
Q Consensus 19 v~~~~~~k~~n~~~~~i~~EDHTL 42 (116)
+++.-.+.. ..+++.+.|+.+||
T Consensus 30 v~v~~~~g~-~~l~i~v~g~~~~L 52 (54)
T PF03633_consen 30 VTVTLLSGD-APLTIKVYGEEVTL 52 (54)
T ss_dssp EEEEEEESS---EEEEETT-----
T ss_pred EEEEEccCC-ccEEEEECCCcccc
Confidence 444433333 57888888888886
No 69
>PRK15197 secreted effector protein PipB; Provisional
Probab=26.47 E-value=3e+02 Score=22.38 Aligned_cols=42 Identities=5% Similarity=0.100 Sum_probs=27.6
Q ss_pred eeeeeecC------CCC-CCceeEEEEEeCCCCCHHHHHHHHHHHHHHH
Q 033562 56 VLFAGYKL------PHP-LQYKIIVRIHTTSQSSPMQAYNQAINDLDKE 97 (116)
Q Consensus 56 V~fAgY~i------pHP-l~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~ 97 (116)
+.|.||.| ||+ ..+++.+.|.-.|..-+.++.++++..+-..
T Consensus 84 ~~~~g~~~~fs~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~r~ 132 (291)
T PRK15197 84 EDVNGCTICLSCGAASENTDPMVIIEVNKNGKTVTDKVDSERFWNVCRM 132 (291)
T ss_pred eecCCeEEEeccCCCcccCCceEEEEEecCCcchHHHHHHHHHHHHHHH
Confidence 67899988 333 3566788888666655666666666555444
No 70
>COG2033 Desulfoferrodoxin [Energy production and conversion]
Probab=26.33 E-value=46 Score=24.11 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=8.8
Q ss_pred eeecCCCCCCce
Q 033562 59 AGYKLPHPLQYK 70 (116)
Q Consensus 59 AgY~ipHPl~~~ 70 (116)
.| .||||++++
T Consensus 57 VG-~IpHPmt~e 67 (126)
T COG2033 57 VG-EIPHPMTPE 67 (126)
T ss_pred Ec-ccCCCCCCc
Confidence 56 899999755
No 71
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=25.14 E-value=2e+02 Score=18.66 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=24.2
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (116)
Q Consensus 72 ~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f 105 (116)
.+++...+. +...|+..|++.|...+.-.++..
T Consensus 60 ~l~a~~~~~-d~y~Aid~a~~klerqL~k~k~k~ 92 (95)
T PRK10470 60 EIHASAEGQ-DMYAAIDGLIDKLARQLTKHKDKL 92 (95)
T ss_pred EEEEEEecC-cHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455665543 888999999988888777776654
No 72
>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=24.95 E-value=1.1e+02 Score=19.36 Aligned_cols=23 Identities=13% Similarity=0.237 Sum_probs=16.1
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHH
Q 033562 72 IVRIHTTSQSSPMQAYNQAINDL 94 (116)
Q Consensus 72 ~lrIqt~~~~~p~e~l~~a~~~l 94 (116)
..+|++.++..-.++|++||+..
T Consensus 8 r~~vkvtp~~~l~~VL~eac~k~ 30 (65)
T PF11470_consen 8 RFKVKVTPNTTLNQVLEEACKKF 30 (65)
T ss_dssp EEEE---TTSBHHHHHHHHHHHT
T ss_pred EEEEEECCCCCHHHHHHHHHHHc
Confidence 46788888878889999999754
No 73
>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=24.91 E-value=1.5e+02 Score=17.22 Aligned_cols=47 Identities=11% Similarity=0.116 Sum_probs=30.4
Q ss_pred hHHHHHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHH
Q 033562 42 IGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAIND 93 (116)
Q Consensus 42 LgNlLr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~ 93 (116)
=.+.++..|.+.|+|.-+-.... .+.+. |..++.....+.+.+++++
T Consensus 12 C~~~v~~~l~~~~GV~~v~vd~~---~~~v~--v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 12 CAKKVEKALSKLPGVKSVKVDLE---TKTVT--VTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp HHHHHHHHHHTSTTEEEEEEETT---TTEEE--EEESTTTSCHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCcEEEEECC---CCEEE--EEEecCCCCHHHHHHHHHH
Confidence 34678899999999977766554 24444 4444432234777777765
No 74
>PRK01215 competence damage-inducible protein A; Provisional
Probab=24.81 E-value=2.6e+02 Score=22.17 Aligned_cols=45 Identities=13% Similarity=0.228 Sum_probs=28.7
Q ss_pred EEEEecCC-cchHHHHHHHhhcCCCeee--e--eecCCCCCCceeEEEEEeCC
Q 033562 32 SFTIEREE-HTIGNILRMQLHRDENVLF--A--GYKLPHPLQYKIIVRIHTTS 79 (116)
Q Consensus 32 ~~~i~~ED-HTLgNlLr~~L~~~~~V~f--A--gY~ipHPl~~~i~lrIqt~~ 79 (116)
++.+.|-+ =+|.-.|.....+.|+|.+ + ||. +|+ ..+.+|+..++
T Consensus 183 ~~~~~Gi~Es~l~~~l~~l~~~~~~~~~~s~p~~~~-~~~--~~v~vrl~~~~ 232 (264)
T PRK01215 183 SILVEGVMESDLAPYVKELVKKYDRVYVKSHPKGYE-VSK--PILEIQIAGSG 232 (264)
T ss_pred EEEECCCCHHHHHHHHHHHHHhCCCCEEecCcccee-cCC--CeEEEEEEEec
Confidence 44555433 4567777777777899987 4 344 343 56777777654
No 75
>PF04263 TPK_catalytic: Thiamin pyrophosphokinase, catalytic domain; InterPro: IPR007371 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0005524 ATP binding, 0009229 thiamine diphosphate biosynthetic process; PDB: 2F17_B 1IG3_B 3S4Y_B 2OMK_B 1IG0_A 3MEL_B 3CQ9_A 3LM8_B 3K94_B 3L8M_B ....
Probab=24.25 E-value=21 Score=25.14 Aligned_cols=16 Identities=25% Similarity=0.339 Sum_probs=10.9
Q ss_pred cCCcchHHHHHHHhhc
Q 033562 37 REEHTIGNILRMQLHR 52 (116)
Q Consensus 37 ~EDHTLgNlLr~~L~~ 52 (116)
.-||||+|+-.-.-.+
T Consensus 97 R~DH~lanl~~l~~~~ 112 (123)
T PF04263_consen 97 RFDHTLANLNLLYKYK 112 (123)
T ss_dssp SHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHH
Confidence 4699999986544333
No 76
>COG0365 Acs Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]
Probab=24.19 E-value=4.3e+02 Score=23.25 Aligned_cols=58 Identities=19% Similarity=0.240 Sum_probs=41.6
Q ss_pred EecCCcchHHH-HHHHhhcCCCeeeeeec-CCCCCCcee-EEEEEeCCCCCHHHHHHHHHHH
Q 033562 35 IEREEHTIGNI-LRMQLHRDENVLFAGYK-LPHPLQYKI-IVRIHTTSQSSPMQAYNQAIND 93 (116)
Q Consensus 35 i~~EDHTLgNl-Lr~~L~~~~~V~fAgY~-ipHPl~~~i-~lrIqt~~~~~p~e~l~~a~~~ 93 (116)
|.--+|.+|.. +-..|.++|.|.-|+-. +|||....+ ...|..+.++.|- .|++-+.+
T Consensus 422 I~vsG~Rig~~EvE~~l~~hP~VaEaAvVg~pd~~kg~~v~afVvL~~g~~~~-~L~~ei~~ 482 (528)
T COG0365 422 IKVSGKRIGPLEIESVLLAHPAVAEAAVVGVPDPGKGQIVLAFVVLAAGVEPN-ELAEEIRR 482 (528)
T ss_pred EeccCeeccHHHHHHHHHhCcceeeeEEEeccCCCCCcEEEEEEEecCCCChH-HHHHHHHH
Confidence 34457888876 77789999999999987 799997664 4455556777776 55554443
No 77
>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=23.40 E-value=2.1e+02 Score=18.20 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=22.3
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033562 72 IVRIHTTSQSSPMQAYNQAINDLDKELDTLKSA 104 (116)
Q Consensus 72 ~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~ 104 (116)
.|++...+ .+...|+..|++.|...+...+++
T Consensus 62 ~l~a~~~~-~d~~~Aid~a~dkl~rql~k~k~k 93 (97)
T PF02482_consen 62 VLVAEESA-EDLYAAIDEAFDKLERQLRKYKEK 93 (97)
T ss_dssp EEEEEEEE-SSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred eEEEEEec-CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444443 389999999998888777666543
No 78
>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=23.32 E-value=1.8e+02 Score=18.39 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=17.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q 033562 81 SSPMQAYNQAINDLDKELDTLK 102 (116)
Q Consensus 81 ~~p~e~l~~a~~~l~~~~~~l~ 102 (116)
.+...|+..|++.|...+...+
T Consensus 70 ~d~~~Aid~a~~kl~rqL~k~k 91 (93)
T cd00552 70 EDLYAAIDLAVDKLERQLRKYK 91 (93)
T ss_pred CCHHHHHHHHHHHHHHHHHHhc
Confidence 4888999999988887776554
No 79
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=22.97 E-value=1.2e+02 Score=23.98 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 82 SPMQAYNQAINDLDKELDTLKSAFE 106 (116)
Q Consensus 82 ~p~e~l~~a~~~l~~~~~~l~~~f~ 106 (116)
+-.+.+.+.++.|...+...++.|.
T Consensus 81 ~~~~~l~~~L~~i~~eF~~~k~~Fl 105 (257)
T PF11348_consen 81 DKAEELAEELEDIKTEFEQEKQDFL 105 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456667777777777766666663
No 80
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=22.93 E-value=3.4e+02 Score=20.54 Aligned_cols=76 Identities=9% Similarity=0.055 Sum_probs=48.1
Q ss_pred eeEEEEecCCcchHHHHHHHhh-cCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 30 AASFTIEREEHTIGNILRMQLH-RDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE 108 (116)
Q Consensus 30 ~~~~~i~~EDHTLgNlLr~~L~-~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a 108 (116)
++++-..+ ++=+.++-..+.. ....+.+|+. |..++ ..-+++.|..+ .+.++++++--.+-|..+.+.++++
T Consensus 153 avtv~~~~-~~~v~Dpt~~Ee~~~~~~l~va~~----~~~~~-i~~i~~~g~~~-~e~~~~~l~~a~~~~~~l~~~~~~~ 225 (230)
T TIGR02065 153 GVAVGKVD-GVVVLDLNEEEDMYGEADMPVAMM----PKLGE-ITLLQLDGDMT-PDEFRQALDLAVKGIKIIYQIQREA 225 (230)
T ss_pred eEEEEEEC-CeEEECCCHHHhhcCCCceEEEEe----CCCCC-EEEEEEecCcC-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444333 3344455555544 3455665554 33333 44566777654 5779999999999999999999988
Q ss_pred HHhh
Q 033562 109 LAKH 112 (116)
Q Consensus 109 ~~~~ 112 (116)
++++
T Consensus 226 l~~~ 229 (230)
T TIGR02065 226 LKNK 229 (230)
T ss_pred HHhh
Confidence 8764
No 81
>PF14185 SpoIISB_antitox: Antitoxin SpoIISB, type II toxin-antitoxin system ; PDB: 3O6Q_B.
Probab=22.64 E-value=17 Score=22.72 Aligned_cols=16 Identities=44% Similarity=0.823 Sum_probs=5.2
Q ss_pred hhcCCCeeeeeecC-CC
Q 033562 50 LHRDENVLFAGYKL-PH 65 (116)
Q Consensus 50 L~~~~~V~fAgY~i-pH 65 (116)
|.+...|.||+|.+ ||
T Consensus 20 lKk~s~~s~a~y~vSPh 36 (56)
T PF14185_consen 20 LKKKSYTSFAEYKVSPH 36 (56)
T ss_dssp EE---SEEE------HH
T ss_pred HHHhhhccccccccChH
Confidence 34456788999986 54
No 82
>PLN02231 alanine transaminase
Probab=22.45 E-value=3.6e+02 Score=23.38 Aligned_cols=57 Identities=7% Similarity=-0.029 Sum_probs=35.2
Q ss_pred HHHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 46 LRMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (116)
Q Consensus 46 Lr~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f 105 (116)
+...|++..+|.+.--+.-.+....-.||+-.- .+.+.|++|+++|.+.++.+-++|
T Consensus 476 ~~~~Ll~~~GV~vvPGs~Fg~~~g~~~~Rit~~---~~~e~l~eal~RL~~~~~~~~~~~ 532 (534)
T PLN02231 476 YCKRLLNATGIVVVPGSGFGQVPGTWHFRCTIL---PQEDKIPAIVSRLTEFHKSFMDEF 532 (534)
T ss_pred HHHHHHHhcCEEEeCCcccCCCCCCCeEEEEeC---CCHHHHHHHHHHHHHHHHHHHHHh
Confidence 445566666665553222223334445777642 577999999999988777776655
No 83
>PF02700 PurS: Phosphoribosylformylglycinamidine (FGAM) synthase; InterPro: IPR003850 Phosphoribosylformylglycinamidine(FGAM) synthetase, 6.3.5.3 from EC, catalyses the fourth step in the de novo purine biosynthetic pathway []. 5-phosphoribosylformylglycinamide (FGAR) + glutamine + ATP = FGAM + glutamate + ADP + Pi In eukaryotes and many bacterial systems (including Escherichia coli and Salmonella typhimurium), the FGAM synthetase is encoded by the large form of PurL (lgPurL), which contains an N-terminal ATPase domain and a C-terminal glutamine-binding domain. In archaeal and other bacterial systems, however, FGAM synthetase is encoded by separate genes, making it a multisubunit (rather than multidomain) enzyme. The protein is composed of the small form of PurL (smPurL), which is homologus to the ATPase domain of lgPurL, PurQ which is homologous to the glutamine-binding domain of of lgPurL, and PurS, whose function is not known. This entry represents the PurS subunit of the multisubunit FGAM synthetase. Recent studies showed that disruption of the purS gene in Bacillus subtilis resulted in a purine auxotrophic phenotype, due to defective FGAM synthetase activity. Therefore, the PurS protein appears to be required for the function of the PurL and PurQ subunits of the FGAM synthetase, but the molecular mechanism for the functional role of PurS is currently not known. For additional information please see [, ].; GO: 0016879 ligase activity, forming carbon-nitrogen bonds; PDB: 2ZW2_B 3D54_B 1VQ3_B 1GTD_A 2YX5_A 2CUW_A 1TWJ_B 1T4A_B 2DGB_B.
Probab=22.40 E-value=1.6e+02 Score=19.29 Aligned_cols=24 Identities=21% Similarity=0.382 Sum_probs=12.9
Q ss_pred eEEEEEeCCCC-CHH-HHHHHHHHHH
Q 033562 71 IIVRIHTTSQS-SPM-QAYNQAINDL 94 (116)
Q Consensus 71 i~lrIqt~~~~-~p~-e~l~~a~~~l 94 (116)
..+.|..++++ ||. +++++|+.++
T Consensus 3 ~~V~V~~K~gvlDPqG~ai~~al~~l 28 (80)
T PF02700_consen 3 VRVEVTLKPGVLDPQGEAIKRALHRL 28 (80)
T ss_dssp EEEEEEE-TTS--HHHHHHHHHHHHT
T ss_pred EEEEEEECCCCcCcHHHHHHHHHHHc
Confidence 34555555553 666 6777776653
No 84
>smart00800 uDENN Domain always found upstream of DENN domain, found in a variety of signalling proteins. The uDENN domain is part of the tripartite DENN domain. It is always found upstream of the DENN domain itself, which is found in a variety of signalling proteins involved in Rab-mediated processes or regulation of MAPKs signalling pathways. The DENN domain is always encircled on both sides by more divergent domains, called uDENN (for upstream DENN) and dDENN (for downstream DENN). The function of the DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity.
Probab=22.31 E-value=1.8e+02 Score=18.75 Aligned_cols=36 Identities=28% Similarity=0.385 Sum_probs=26.3
Q ss_pred CCccccceeeCCCCeeeEeeccCCCcceeEEEEecCC
Q 033562 3 APDRYERFVVPEGTKKVSYERDTKIINAASFTIEREE 39 (116)
Q Consensus 3 ~p~~~~~~~l~~~~~Kv~~~~~~k~~n~~~~~i~~ED 39 (116)
.|+...+|-+|+|..-.. ..+...+..-+|++.++|
T Consensus 42 ~~~~i~~FCfP~G~~~~~-~~~~~~~~~f~FvLT~~d 77 (89)
T smart00800 42 LPDSIPLFCFPEGLLFVT-QKSSKDPQFFSFVLTDID 77 (89)
T ss_pred CccCCCeeECCCCeEeec-ccCCCCCcEEEEEEECCC
Confidence 355678888999876654 344566778889998887
No 85
>PRK05783 hypothetical protein; Provisional
Probab=22.20 E-value=1.5e+02 Score=19.84 Aligned_cols=25 Identities=8% Similarity=0.113 Sum_probs=15.7
Q ss_pred eeEEEEEeCCCC-CHH-HHHHHHHHHH
Q 033562 70 KIIVRIHTTSQS-SPM-QAYNQAINDL 94 (116)
Q Consensus 70 ~i~lrIqt~~~~-~p~-e~l~~a~~~l 94 (116)
++.+.|..++|+ ||. +|+++|+..+
T Consensus 4 k~~V~V~lK~gVlDPqG~aI~~aL~~l 30 (84)
T PRK05783 4 YVELIIINKDSVRDPEGETIQRYVIER 30 (84)
T ss_pred EEEEEEEECCCCcCchHHHHHHHHHHc
Confidence 345556666654 776 7777777554
No 86
>PRK15202 type III secretion chaperone protein SigE; Provisional
Probab=21.79 E-value=3.1e+02 Score=19.59 Aligned_cols=75 Identities=20% Similarity=0.308 Sum_probs=48.5
Q ss_pred CCCCeeeEeeccCCCcceeEEEEecCCcchH------------HHHHHHhhcC------------CCeeeeeecCCCCCC
Q 033562 13 PEGTKKVSYERDTKIINAASFTIEREEHTIG------------NILRMQLHRD------------ENVLFAGYKLPHPLQ 68 (116)
Q Consensus 13 ~~~~~Kv~~~~~~k~~n~~~~~i~~EDHTLg------------NlLr~~L~~~------------~~V~fAgY~ipHPl~ 68 (116)
|++++-+.+- +.+.+-|..+||+|- |-|.+.|.-+ ..+..|-|+.|
T Consensus 17 ~~depaliid------ddi~IYfnes~~~lem~CPf~~LPdn~~~Lq~~LsLNYas~V~la~Dae~t~L~Al~rlp---- 86 (117)
T PRK15202 17 PEDEPALIID------DDIQIYFNESDHTLEMCCPFMPLPDNILTLQHFLSLNYTSAVTLAADAENTALVALYRLP---- 86 (117)
T ss_pred CCCCceEEec------CCeEEEEccCCcchhccCCcccCCccHHHHHHHHhhcccCceEEEEcCCCceEEEeeecC----
Confidence 4555555543 558899999999873 4456666544 23344445555
Q ss_pred ceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 69 YKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE 108 (116)
Q Consensus 69 ~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a 108 (116)
+.+-.+-+.-+.+-.++..+.++++|.+.
T Consensus 87 -----------~~s~~ee~~~g~e~fIs~vr~L~~~~a~r 115 (117)
T PRK15202 87 -----------QTSTEEEALTGFELFISNVKQLKEEYARR 115 (117)
T ss_pred -----------CCCcHHHHHhhHHHHHHHHHHHHHHHhhc
Confidence 23445666677888888888888887653
No 87
>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=21.70 E-value=1.6e+02 Score=16.17 Aligned_cols=28 Identities=29% Similarity=0.379 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033562 85 QAYNQAINDLDKELDTLKSAFEAELAKH 112 (116)
Q Consensus 85 e~l~~a~~~l~~~~~~l~~~f~~a~~~~ 112 (116)
..|..+|..++..+......|..=-.+|
T Consensus 2 ~~l~a~I~~~r~~f~~~~~aF~aY~~~F 29 (32)
T PF05465_consen 2 SDLLAAIAEFREEFDDTQDAFEAYADEF 29 (32)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3566777777777777777776654444
No 88
>KOG0758 consensus Mitochondrial carnitine-acylcarnitine carrier protein [Energy production and conversion]
Probab=21.10 E-value=1.4e+02 Score=24.65 Aligned_cols=34 Identities=18% Similarity=0.377 Sum_probs=23.2
Q ss_pred eeeecCCCCCCceeEEEEEeCCCCC---HHHHHHHHHH
Q 033562 58 FAGYKLPHPLQYKIIVRIHTTSQSS---PMQAYNQAIN 92 (116)
Q Consensus 58 fAgY~ipHPl~~~i~lrIqt~~~~~---p~e~l~~a~~ 92 (116)
.|+--|-||++ -+.+|+||-.... ..+++++.+.
T Consensus 25 ~~~vlVGhPfD-TvKVRlQt~~~~~y~~~~~c~~~t~~ 61 (297)
T KOG0758|consen 25 AAQVLVGHPFD-TVKVRLQTQNTPVYKGTLDCVKKTLK 61 (297)
T ss_pred hhhhhccCCcc-ceEEeeeccCCCCcccHHHHHHHHHH
Confidence 36667899986 6899999975422 3555555544
No 89
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=20.91 E-value=3.1e+02 Score=19.25 Aligned_cols=35 Identities=14% Similarity=0.220 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhhh
Q 033562 79 SQSSPMQAYNQAINDLDK-ELDTLKSAFEAELAKHS 113 (116)
Q Consensus 79 ~~~~p~e~l~~a~~~l~~-~~~~l~~~f~~a~~~~~ 113 (116)
|.++|.++|.+..+.|.+ -++.+..++.+.+..|.
T Consensus 95 G~vd~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~ 130 (134)
T PF12010_consen 95 GLVDPEEALPEFNEKLKAAGIDKVIAELQKQLDAFL 130 (134)
T ss_pred cCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHH
Confidence 345677777777666543 25556666666666664
No 90
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=20.60 E-value=1.7e+02 Score=20.70 Aligned_cols=52 Identities=25% Similarity=0.455 Sum_probs=35.3
Q ss_pred hHHHHHHHhhcCCCee--eeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 42 IGNILRMQLHRDENVL--FAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAFEAE 108 (116)
Q Consensus 42 LgNlLr~~L~~~~~V~--fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f~~a 108 (116)
+.+++|..|++-+-|. ..||-- | ...|.+.|++-=+.+.+.++.+++.|..+
T Consensus 57 v~~l~rrGll~relvqkgWvGYiy-------------a--~~~P~k~leei~~~i~keiEelEk~~k~e 110 (113)
T COG5625 57 VAVLLRRGLLARELVQKGWVGYIY-------------A--TTPPPKPLEEIEEEIMKEIEELEKEFKNE 110 (113)
T ss_pred HHHHHHhhHHHHHHHhccceeeEe-------------c--CCCCchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566666666533332 556632 2 23688888888888999999999998764
No 91
>PTZ00377 alanine aminotransferase; Provisional
Probab=20.54 E-value=4.5e+02 Score=22.01 Aligned_cols=56 Identities=7% Similarity=0.087 Sum_probs=33.9
Q ss_pred HHHhhcCCCeeeeeecCCCCCCceeEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033562 47 RMQLHRDENVLFAGYKLPHPLQYKIIVRIHTTSQSSPMQAYNQAINDLDKELDTLKSAF 105 (116)
Q Consensus 47 r~~L~~~~~V~fAgY~ipHPl~~~i~lrIqt~~~~~p~e~l~~a~~~l~~~~~~l~~~f 105 (116)
...+++..+|.+..-..-.+....-.+||-.. .+.+.+++|+++|.+.++.+.++|
T Consensus 425 ~~~ll~~~gV~v~pG~~F~~~~~~~~~Rls~~---~~~e~l~~~l~rl~~~~~~~~~~~ 480 (481)
T PTZ00377 425 CLELLESTGIVVVPGSGFGQKPGTYHFRITIL---PPEEQIEEMVKKIKEFHESFMKKY 480 (481)
T ss_pred HHHHHHHcCEEEeCCcccCCCCCCCEEEEEEC---CCHHHHHHHHHHHHHHHHHHHHhh
Confidence 34556666766553332222222346777764 356889999999988777665554
No 92
>KOG1507 consensus Nucleosome assembly protein NAP-1 [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=20.21 E-value=1.2e+02 Score=25.62 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 033562 88 NQAINDLDKELDTLKSAFEAELAKHSRV 115 (116)
Q Consensus 88 ~~a~~~l~~~~~~l~~~f~~a~~~~~~~ 115 (116)
-.|++.|+..|.+++.+|.+++-+...+
T Consensus 79 v~aLk~lQ~~~~~ie~~F~~e~~~LE~k 106 (358)
T KOG1507|consen 79 VLALKNLQLECDEIEAKFQEEVHELERK 106 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4588889999999999999887654433
No 93
>PF02777 Sod_Fe_C: Iron/manganese superoxide dismutases, C-terminal domain Note: SCOP classifies the two domains separately.; InterPro: IPR019832 Superoxide dismutases (SODs) (1.15.1.1 from EC) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [, , ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers. The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) []. This entry represents the C-terminal domain of Manganese/iron superoxide dismutase. ; GO: 0004784 superoxide dismutase activity, 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 1KKC_Y 2GOJ_B 1UES_C 1UER_C 1QNN_A 1MY6_A 1MA1_F 1P7G_Q 3EVK_D 2GPC_A ....
Probab=20.04 E-value=1.2e+02 Score=20.35 Aligned_cols=30 Identities=23% Similarity=0.316 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033562 82 SPMQAYNQAINDLDKELDTLKSAFEAELAK 111 (116)
Q Consensus 82 ~p~e~l~~a~~~l~~~~~~l~~~f~~a~~~ 111 (116)
.|-..|.++|+.=-.-++.++++|.++...
T Consensus 2 ~P~g~l~~~I~~~FGS~d~fk~~f~~~a~~ 31 (106)
T PF02777_consen 2 KPSGKLKKAIEEDFGSFDNFKAEFTAAALS 31 (106)
T ss_dssp S-THHHHHHHHHHHSSHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence 577889999999889999999999887654
Done!