Query 033968
Match_columns 107
No_of_seqs 115 out of 485
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:18:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033968.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033968hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07029 RNAP_I_III_AC19 AC19 s 100.0 1.4E-36 3.1E-41 203.4 10.6 83 3-85 2-85 (85)
2 PF13656 RNA_pol_L_2: RNA poly 100.0 1.8E-36 4E-41 199.3 8.8 76 10-85 1-77 (77)
3 KOG3438 DNA-directed RNA polym 100.0 1.8E-35 4E-40 203.7 11.1 96 1-96 7-103 (105)
4 PRK01146 DNA-directed RNA poly 100.0 6E-35 1.3E-39 195.5 9.9 78 6-83 7-85 (85)
5 cd06927 RNAP_L L subunit of Ar 100.0 6.4E-35 1.4E-39 194.6 9.9 78 6-83 5-83 (83)
6 cd07027 RNAP_RPB11_like RPB11 100.0 9.7E-35 2.1E-39 193.8 10.1 77 6-82 5-82 (83)
7 cd06926 RNAP_II_RPB11 RPB11 su 100.0 1.5E-34 3.3E-39 196.3 10.4 81 5-85 12-93 (93)
8 COG1761 RPB11 DNA-directed RNA 100.0 7.1E-32 1.5E-36 185.5 11.7 86 6-92 11-97 (99)
9 KOG4392 RNA polymerase, subuni 100.0 3.5E-30 7.7E-35 180.2 10.8 86 6-91 25-111 (117)
10 cd00460 RNAP_RPB11_RPB3 RPB11 99.9 3.7E-26 8E-31 152.3 9.5 75 6-81 5-86 (86)
11 PF01193 RNA_pol_L: RNA polyme 99.7 3.3E-17 7.1E-22 104.0 4.7 64 12-79 1-66 (66)
12 PRK14979 DNA-directed RNA poly 95.1 0.097 2.1E-06 39.9 6.7 39 49-87 149-188 (195)
13 cd07028 RNAP_RPB3_like RPB3 su 95.0 0.066 1.4E-06 41.0 5.6 47 36-83 164-211 (212)
14 smart00662 RPOLD RNA polymeras 94.4 0.089 1.9E-06 40.3 4.9 32 49-80 191-223 (224)
15 cd06928 RNAP_alpha_NTD N-termi 94.2 0.094 2E-06 40.1 4.7 43 37-79 164-213 (215)
16 TIGR02027 rpoA DNA-directed RN 93.9 0.17 3.7E-06 40.5 5.9 47 37-83 155-208 (297)
17 cd07031 RNAP_II_RPB3 RPB3 subu 93.5 0.14 3E-06 40.4 4.6 52 36-87 201-264 (265)
18 PRK00783 DNA-directed RNA poly 93.2 0.087 1.9E-06 40.9 3.1 28 7-34 8-35 (263)
19 PRK05182 DNA-directed RNA poly 92.7 0.32 6.9E-06 39.2 5.7 47 37-83 172-225 (310)
20 cd07028 RNAP_RPB3_like RPB3 su 92.6 0.14 3E-06 39.3 3.3 31 6-36 7-38 (212)
21 cd06928 RNAP_alpha_NTD N-termi 92.3 0.21 4.5E-06 38.2 4.0 39 7-45 6-49 (215)
22 CHL00013 rpoA RNA polymerase a 92.2 0.35 7.6E-06 39.5 5.4 47 37-83 171-223 (327)
23 cd07030 RNAP_D D subunit of Ar 91.9 0.17 3.8E-06 39.2 3.1 28 7-34 8-35 (259)
24 PRK14979 DNA-directed RNA poly 90.6 0.32 6.8E-06 37.1 3.4 36 5-41 9-45 (195)
25 smart00662 RPOLD RNA polymeras 89.8 0.45 9.7E-06 36.4 3.6 33 12-44 2-35 (224)
26 PRK05182 DNA-directed RNA poly 89.2 0.59 1.3E-05 37.7 4.1 38 8-45 17-59 (310)
27 PRK00783 DNA-directed RNA poly 88.9 1.2 2.5E-05 34.6 5.4 40 48-87 221-261 (263)
28 cd07031 RNAP_II_RPB3 RPB3 subu 85.5 0.9 2E-05 35.8 3.1 32 7-38 8-40 (265)
29 cd07030 RNAP_D D subunit of Ar 84.8 2.3 5.1E-05 32.9 5.1 36 49-84 222-258 (259)
30 COG0202 RpoA DNA-directed RNA 84.2 0.96 2.1E-05 36.7 2.8 29 8-36 17-46 (317)
31 cd07032 RNAP_I_II_AC40 AC40 su 83.5 2.9 6.4E-05 33.7 5.3 37 47-83 253-290 (291)
32 CHL00013 rpoA RNA polymerase a 83.1 1 2.2E-05 36.8 2.5 40 7-46 17-61 (327)
33 TIGR02027 rpoA DNA-directed RN 79.2 1.6 3.4E-05 35.0 2.3 29 17-45 11-40 (297)
34 cd04905 ACT_CM-PDT C-terminal 71.5 21 0.00047 22.2 5.8 67 11-79 3-71 (80)
35 COG2805 PilT Tfp pilus assembl 67.9 3.3 7E-05 34.4 1.6 23 19-41 183-205 (353)
36 PRK02261 methylaspartate mutas 63.2 7.7 0.00017 27.5 2.6 37 9-45 4-42 (137)
37 TIGR02370 pyl_corrinoid methyl 61.0 10 0.00022 28.2 3.0 40 8-47 84-125 (197)
38 cd02070 corrinoid_protein_B12- 60.2 26 0.00055 25.9 5.1 40 8-47 82-123 (201)
39 PF10824 DUF2580: Protein of u 58.6 43 0.00093 20.9 5.6 42 62-103 57-98 (100)
40 PF06657 Cep57_MT_bd: Centroso 56.5 48 0.001 21.6 5.4 36 62-97 10-45 (79)
41 cd02071 MM_CoA_mut_B12_BD meth 56.1 30 0.00066 23.5 4.6 27 12-38 3-29 (122)
42 cd02069 methionine_synthase_B1 55.1 14 0.0003 28.1 3.0 41 7-47 87-129 (213)
43 cd02067 B12-binding B12 bindin 52.4 40 0.00087 22.3 4.6 26 12-37 3-28 (119)
44 PRK00549 competence damage-ind 49.9 86 0.0019 26.1 7.1 39 21-63 191-229 (414)
45 KOG2972 Uncharacterized conser 49.0 44 0.00095 27.0 5.0 52 22-73 93-146 (276)
46 cd04880 ACT_AAAH-PDT-like ACT 48.3 61 0.0013 19.7 5.2 67 12-79 2-69 (75)
47 PLN02231 alanine transaminase 47.3 83 0.0018 27.0 6.8 58 27-86 476-533 (534)
48 KOG1522 RNA polymerase II, sub 42.9 52 0.0011 26.6 4.5 66 25-90 187-270 (285)
49 COG1027 AspA Aspartate ammonia 42.3 62 0.0014 27.9 5.1 67 23-94 112-181 (471)
50 PF12909 DUF3832: Protein of u 39.5 59 0.0013 21.9 3.8 34 56-89 28-61 (89)
51 PRK12729 fliE flagellar hook-b 38.4 80 0.0017 22.7 4.5 18 32-50 10-27 (127)
52 PF04368 DUF507: Protein of un 37.3 1.4E+02 0.0031 22.5 6.0 37 58-94 120-156 (183)
53 PTZ00377 alanine aminotransfer 37.0 1.6E+02 0.0035 24.4 6.8 57 27-85 424-480 (481)
54 PF04340 DUF484: Protein of un 36.4 1.3E+02 0.0028 22.6 5.7 38 60-97 38-75 (225)
55 KOG0758 Mitochondrial carnitin 36.2 42 0.00092 27.4 3.1 32 40-72 26-61 (297)
56 COG5211 SSU72 RNA polymerase I 36.2 2E+02 0.0042 22.0 6.6 81 17-97 72-186 (197)
57 cd01406 SIR2-like Sir2-like: P 35.9 44 0.00096 25.0 3.1 42 3-47 143-192 (242)
58 TIGR00741 yfiA ribosomal subun 35.9 1.2E+02 0.0025 19.3 5.1 33 53-85 60-92 (95)
59 PF02482 Ribosomal_S30AE: Sigm 35.6 1.2E+02 0.0025 19.2 4.7 31 53-83 62-92 (97)
60 PRK10470 ribosome hibernation 34.9 1.3E+02 0.0027 19.4 5.1 33 53-85 60-92 (95)
61 PF12179 IKKbetaNEMObind: I-ka 34.5 96 0.0021 17.9 3.7 32 73-104 3-34 (38)
62 PRK01215 competence damage-ind 34.1 2.3E+02 0.005 22.2 7.6 46 13-61 183-233 (264)
63 PRK00407 hypothetical protein; 33.7 75 0.0016 22.6 3.8 34 41-78 3-37 (139)
64 PF13851 GAS: Growth-arrest sp 33.1 1.3E+02 0.0027 22.7 5.2 34 64-97 109-142 (201)
65 COG2804 PulE Type II secretory 32.8 37 0.00081 29.6 2.5 24 18-41 311-334 (500)
66 PF11598 COMP: Cartilage oligo 31.6 1.2E+02 0.0025 18.0 4.8 31 63-93 2-32 (45)
67 COG5015 Uncharacterized conser 31.4 34 0.00073 24.8 1.7 29 26-59 48-76 (132)
68 COG0634 Hpt Hypoxanthine-guani 30.4 55 0.0012 24.9 2.8 20 16-35 102-121 (178)
69 COG0202 RpoA DNA-directed RNA 30.4 97 0.0021 25.2 4.4 39 50-88 188-227 (317)
70 KOG0427 Ubiquitin conjugating 30.2 1.4E+02 0.003 22.0 4.7 49 32-80 75-126 (161)
71 PRK10553 assembly protein for 30.0 1.7E+02 0.0037 19.4 5.0 35 24-61 19-53 (87)
72 COG2033 Desulfoferrodoxin [Ene 29.1 38 0.00083 24.4 1.6 12 40-52 57-68 (126)
73 COG3062 NapD Uncharacterized p 29.0 1.6E+02 0.0034 20.3 4.5 34 24-61 20-53 (94)
74 TIGR01546 GAPDH-II_archae glyc 28.3 1.6E+02 0.0034 24.2 5.3 51 21-73 190-240 (333)
75 cd00552 RaiA RaiA ("ribosome-a 28.0 1.3E+02 0.0029 18.9 4.0 23 60-82 69-91 (93)
76 cd04908 ACT_Bt0572_1 N-termina 27.0 1.4E+02 0.0031 17.6 5.5 46 12-60 4-49 (66)
77 PF02777 Sod_Fe_C: Iron/mangan 26.8 90 0.002 20.7 3.1 30 62-91 2-31 (106)
78 COG4495 Uncharacterized protei 26.5 1.5E+02 0.0033 20.8 4.2 59 28-91 29-91 (109)
79 cd07032 RNAP_I_II_AC40 AC40 su 26.0 80 0.0017 25.5 3.1 28 7-34 8-35 (291)
80 cd07367 CarBb CarBb is the B s 25.6 1.1E+02 0.0024 23.8 3.9 33 39-78 5-38 (268)
81 PRK10963 hypothetical protein; 25.3 1.4E+02 0.003 22.7 4.2 60 26-97 7-72 (223)
82 PRK15197 secreted effector pro 25.0 3.2E+02 0.0069 22.1 6.4 41 37-77 84-132 (291)
83 PF03927 NapD: NapD protein; 25.0 1.2E+02 0.0025 19.5 3.3 34 24-61 17-50 (79)
84 PF00437 T2SE: Type II/IV secr 24.3 1.5E+02 0.0032 22.3 4.2 33 9-41 172-204 (270)
85 KOG4014 Uncharacterized conser 24.3 1.4E+02 0.003 23.6 4.0 29 69-97 35-63 (248)
86 COG4115 Uncharacterized protei 24.2 68 0.0015 21.6 2.0 24 25-51 28-51 (84)
87 PF09236 AHSP: Alpha-haemoglob 23.6 2.1E+02 0.0046 19.4 4.4 31 65-95 57-87 (89)
88 PF02700 PurS: Phosphoribosylf 23.4 1.3E+02 0.0028 19.6 3.2 23 52-74 3-28 (80)
89 COG1058 CinA Predicted nucleot 23.3 3.3E+02 0.0071 21.6 6.1 66 12-79 181-247 (255)
90 cd02116 ACT ACT domains are co 23.3 1.2E+02 0.0025 15.2 6.7 48 13-61 2-49 (60)
91 COG0529 CysC Adenylylsulfate k 23.3 1.6E+02 0.0035 22.8 4.2 38 38-75 153-190 (197)
92 PHA02766 hypothetical protein; 23.1 73 0.0016 20.4 1.9 50 11-72 16-66 (73)
93 PF12010 DUF3502: Domain of un 22.7 2.7E+02 0.0059 19.3 5.4 34 62-95 98-132 (134)
94 PRK13364 protocatechuate 4,5-d 22.6 1.3E+02 0.0028 23.9 3.7 41 39-80 5-46 (278)
95 PRK14891 50S ribosomal protein 22.5 43 0.00094 24.3 0.9 23 33-56 3-25 (131)
96 PF05465 Halo_GVPC: Halobacter 22.1 1.5E+02 0.0033 16.2 3.8 28 65-92 2-29 (32)
97 PF13289 SIR2_2: SIR2-like dom 21.8 95 0.0021 20.6 2.5 26 21-47 74-99 (143)
98 PF00403 HMA: Heavy-metal-asso 21.6 1.8E+02 0.0038 16.8 5.5 45 24-73 13-58 (62)
99 KOG2070 Guanine nucleotide exc 21.4 2.6E+02 0.0057 25.0 5.5 44 52-95 605-649 (661)
100 PF10203 Pet191_N: Cytochrome 21.2 49 0.0011 21.1 0.9 30 59-88 25-54 (68)
101 cd00529 RuvC_resolvase Hollida 21.0 2.9E+02 0.0062 19.5 5.0 29 33-61 5-37 (154)
102 COG4245 TerY Uncharacterized p 20.6 1.9E+02 0.0041 22.5 4.1 28 52-79 6-36 (207)
103 cd07931 eukaryotic_phosphagen_ 20.4 4.3E+02 0.0094 21.8 6.4 21 54-74 209-231 (338)
104 PRK03987 translation initiatio 20.4 4.2E+02 0.0092 20.8 6.2 45 33-80 205-250 (262)
105 PF07083 DUF1351: Protein of u 20.3 3.4E+02 0.0073 20.6 5.5 37 62-98 71-107 (215)
106 KOG0762 Mitochondrial carrier 20.2 84 0.0018 25.6 2.2 23 40-63 25-48 (311)
107 COG0049 RpsG Ribosomal protein 20.2 74 0.0016 23.5 1.7 16 60-75 54-69 (148)
108 PF06013 WXG100: Proteins of 1 20.1 2E+02 0.0044 16.9 5.0 30 65-94 54-83 (86)
No 1
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=100.00 E-value=1.4e-36 Score=203.39 Aligned_cols=83 Identities=49% Similarity=0.907 Sum_probs=80.3
Q ss_pred CCCCCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHH
Q 033968 3 HGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHV 81 (107)
Q Consensus 3 ~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l 81 (107)
.+.++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|+++
T Consensus 2 ~~~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~ 81 (85)
T cd07029 2 EGEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHI 81 (85)
T ss_pred CcccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999997 99999999999999999999
Q ss_pred HHHH
Q 033968 82 RSTF 85 (107)
Q Consensus 82 ~~~f 85 (107)
++.|
T Consensus 82 ~~~f 85 (85)
T cd07029 82 LSTF 85 (85)
T ss_pred HhcC
Confidence 9876
No 2
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=100.00 E-value=1.8e-36 Score=199.29 Aligned_cols=76 Identities=39% Similarity=0.824 Sum_probs=71.9
Q ss_pred CeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 10 SNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTF 85 (107)
Q Consensus 10 n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f 85 (107)
|+++|+|.+|||||||+||++|+++|+|.||||+|||||+++++|||||+++ +|.+||++|+++|.++|++++++|
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 7899999999999999999999999999999999999999999999999999 999999999999999999999988
No 3
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=1.8e-35 Score=203.68 Aligned_cols=96 Identities=50% Similarity=0.952 Sum_probs=91.8
Q ss_pred CCCCCCCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968 1 MEHGAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCR 79 (107)
Q Consensus 1 ~~~~~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~ 79 (107)
|.+++..+.++.+|++..|||||||+||++|+++|.|+||||.||||++++++|||||.++ +++++|++||++|.+.|+
T Consensus 7 m~~~~~~d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~ 86 (105)
T KOG3438|consen 7 MSQASFTDLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCD 86 (105)
T ss_pred hccCcccCCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHH
Confidence 5678888999999999999999999999999999999999999999999999999999977 999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 033968 80 HVRSTFAKAVDDFRTSE 96 (107)
Q Consensus 80 ~l~~~f~~a~~~~~~~~ 96 (107)
+++..|.+++++|+...
T Consensus 87 ~v~~kF~~~i~~~k~~~ 103 (105)
T KOG3438|consen 87 HVRSKFEEEIEEYKDQK 103 (105)
T ss_pred HHHHHHHHHHHHhhhhc
Confidence 99999999999998654
No 4
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=100.00 E-value=6e-35 Score=195.51 Aligned_cols=78 Identities=26% Similarity=0.458 Sum_probs=74.9
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
.+++|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++ +|.+||++|+++|.+.|++|++
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 46789999999999999999999999999999999999999999999999999977 9999999999999999999863
No 5
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=100.00 E-value=6.4e-35 Score=194.63 Aligned_cols=78 Identities=27% Similarity=0.474 Sum_probs=74.9
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
.+++|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++ +|.+||++|+++|++.|+++++
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 46789999999999999999999999999999999999999999999999999997 9999999999999999999863
No 6
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=100.00 E-value=9.7e-35 Score=193.76 Aligned_cols=77 Identities=31% Similarity=0.520 Sum_probs=74.4
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHH
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVR 82 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~ 82 (107)
+.++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|++++
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 46789999999999999999999999999999999999999999999999999997 999999999999999999985
No 7
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=100.00 E-value=1.5e-34 Score=196.26 Aligned_cols=81 Identities=36% Similarity=0.683 Sum_probs=78.4
Q ss_pred CCCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 5 AFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 5 ~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
-++.+|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++ +|.+||++|+++|.+.|+++++
T Consensus 12 d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~~ 91 (93)
T cd06926 12 DTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITDLISELSLLKE 91 (93)
T ss_pred cCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 368899999999999999999999999999999999999999999999999999997 9999999999999999999998
Q ss_pred HH
Q 033968 84 TF 85 (107)
Q Consensus 84 ~f 85 (107)
.|
T Consensus 92 ~f 93 (93)
T cd06926 92 EF 93 (93)
T ss_pred hC
Confidence 76
No 8
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=99.98 E-value=7.1e-32 Score=185.53 Aligned_cols=86 Identities=30% Similarity=0.490 Sum_probs=82.6
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST 84 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~ 84 (107)
.+++|+++|+|.||||||||+||++|++||+|.||||+||||+.++++|||||+++ +|.+||++|++.+.+.|++|.++
T Consensus 11 ~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~~ 90 (99)
T COG1761 11 KKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARKILKDLEELLDQ 90 (99)
T ss_pred ccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 36799999999999999999999999999999999999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHH
Q 033968 85 FAKAVDDF 92 (107)
Q Consensus 85 f~~a~~~~ 92 (107)
| ++++++
T Consensus 91 ~-~~~e~~ 97 (99)
T COG1761 91 F-EEFEKK 97 (99)
T ss_pred H-HHHHhh
Confidence 9 887765
No 9
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=99.97 E-value=3.5e-30 Score=180.17 Aligned_cols=86 Identities=33% Similarity=0.555 Sum_probs=84.1
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST 84 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~ 84 (107)
++.+|++.|+|++|||||||+||.+|++||+|.||||++|||++.++.|||||..+ +|.++|.+|+.+|...++.++.+
T Consensus 25 tKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~~~ 104 (117)
T KOG4392|consen 25 TKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTEDCSPADALTNAITDLIEELSLLENR 104 (117)
T ss_pred CCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999988 99999999999999999999999
Q ss_pred HHHHHHH
Q 033968 85 FAKAVDD 91 (107)
Q Consensus 85 f~~a~~~ 91 (107)
|..+++.
T Consensus 105 f~~~~~~ 111 (117)
T KOG4392|consen 105 FKAEAAL 111 (117)
T ss_pred HHHHHhc
Confidence 9999987
No 10
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=99.94 E-value=3.7e-26 Score=152.33 Aligned_cols=75 Identities=31% Similarity=0.539 Sum_probs=71.6
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCC------CCceeEEEEeCCC-CHHHHHHHHHHHHHHHH
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPS------DARVNIRVQTTGD-PAREVLKDSCQELMLMC 78 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl------e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~ 78 (107)
.+++|+++|+|.||||||||+||++|++ |.|.||||+||||+ .+++.|+|+|+|+ +|.+||++|++.|.+.|
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 4678999999999999999999999999 99999999999999 9999999999998 99999999999999998
Q ss_pred HHH
Q 033968 79 RHV 81 (107)
Q Consensus 79 ~~l 81 (107)
+.|
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=99.69 E-value=3.3e-17 Score=103.96 Aligned_cols=64 Identities=34% Similarity=0.517 Sum_probs=60.2
Q ss_pred eEEEEecCCcchHHHHHHHHhcC-CCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968 12 ATFSLTEEDHTLANAVRFTLNQD-PRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCR 79 (107)
Q Consensus 12 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~ 79 (107)
++|.+.|+|||+||+||..|+++ |.|.+++ ||..+++.|+|+|+|+ +|.++|.+|++.|.+.|+
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~ 66 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLTPKEALLKAIKILKEKLN 66 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence 57999999999999999999999 9999999 9999999999999999 999999999999998773
No 12
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=95.13 E-value=0.097 Score=39.89 Aligned_cols=39 Identities=15% Similarity=0.296 Sum_probs=35.1
Q ss_pred CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK 87 (107)
Q Consensus 49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~ 87 (107)
.++..|.|.|+|. +|.+||..|++-|.+.++.|.+.++.
T Consensus 149 ~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~ 188 (195)
T PRK14979 149 NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEG 188 (195)
T ss_pred CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4899999999999 99999999999999999998776653
No 13
>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=95.02 E-value=0.066 Score=41.05 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=40.3
Q ss_pred CeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 36 RVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 36 ~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
=|.-|.|++. |-.++..|.|.|+|. +|.+||.+|++-|++.++.|.+
T Consensus 164 PV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~ 211 (212)
T cd07028 164 PVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL 211 (212)
T ss_pred CceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence 3566778854 466899999999999 9999999999999999998875
No 14
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=94.39 E-value=0.089 Score=40.28 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=29.1
Q ss_pred CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHH
Q 033968 49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRH 80 (107)
Q Consensus 49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~ 80 (107)
.+++.|.|.|+|. +|.+||.+|++-|.+.++.
T Consensus 191 ~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~ 223 (224)
T smart00662 191 YDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 223 (224)
T ss_pred CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence 5789999999999 9999999999999987764
No 15
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=94.17 E-value=0.094 Score=40.06 Aligned_cols=43 Identities=19% Similarity=0.287 Sum_probs=35.0
Q ss_pred eeeeeecCCC------CCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968 37 VTFCGYSIPH------PSDARVNIRVQTTGD-PAREVLKDSCQELMLMCR 79 (107)
Q Consensus 37 V~fAgY~vpH------Ple~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~ 79 (107)
|.-+.|.|.- .-..++.|.|.|+|. +|.+||..|++.|.+.+.
T Consensus 164 V~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~ 213 (215)
T cd06928 164 VRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFS 213 (215)
T ss_pred eEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhh
Confidence 5666777543 234678999999999 999999999999988775
No 16
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=93.93 E-value=0.17 Score=40.50 Aligned_cols=47 Identities=11% Similarity=0.277 Sum_probs=38.4
Q ss_pred eeeeeecCCC------CCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 37 VTFCGYSIPH------PSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 37 V~fAgY~vpH------Ple~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
|.-+.|.|.. ...+++.|.|.|+|. +|.+||.+|++-|.+.+..|.+
T Consensus 155 V~~Vny~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 155 VLKVNYEVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred eEEEEEEEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 5556676653 234689999999999 9999999999999999998865
No 17
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=93.53 E-value=0.14 Score=40.40 Aligned_cols=52 Identities=13% Similarity=0.209 Sum_probs=42.9
Q ss_pred CeeeeeecCCCCC-----------CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 36 RVTFCGYSIPHPS-----------DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK 87 (107)
Q Consensus 36 ~V~fAgY~vpHPl-----------e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~ 87 (107)
...||...+.||- .+++.|.|.|.|. +|.++|.+|++-|.+.++.|.+.++.
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 4556666666652 5778999999999 99999999999999999999988754
No 18
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=93.24 E-value=0.087 Score=40.91 Aligned_cols=28 Identities=29% Similarity=0.345 Sum_probs=23.8
Q ss_pred CCCCeeEEEEecCCcchHHHHHHHHhcC
Q 033968 7 GDQSNATFSLTEEDHTLANAVRFTLNQD 34 (107)
Q Consensus 7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~ 34 (107)
.+++.++|.+.|-++||||+||-.|+..
T Consensus 8 ~~~~~~~f~~~g~~~t~~NalRRvlls~ 35 (263)
T PRK00783 8 LDDRSARFVVEGVTPAFANAIRRAMIAD 35 (263)
T ss_pred cCCcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence 3567889999999999999999888875
No 19
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=92.70 E-value=0.32 Score=39.25 Aligned_cols=47 Identities=17% Similarity=0.229 Sum_probs=38.5
Q ss_pred eeeeeecCCCC------CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 37 VTFCGYSIPHP------SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 37 V~fAgY~vpHP------le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
|.-+.|.|.-. -..++.|.|.|+|. +|.+||.+|+..|...+..|.+
T Consensus 172 V~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~ 225 (310)
T PRK05182 172 VKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD 225 (310)
T ss_pred ccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 55667766542 13579999999999 9999999999999999988765
No 20
>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=92.61 E-value=0.14 Score=39.31 Aligned_cols=31 Identities=32% Similarity=0.465 Sum_probs=26.9
Q ss_pred CCCCCeeEEEEecCCcchHHHHHHHHhcC-CC
Q 033968 6 FGDQSNATFSLTEEDHTLANAVRFTLNQD-PR 36 (107)
Q Consensus 6 ~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~ 36 (107)
..+++.+.|.+.|-|+|+||+||-.|+.. |.
T Consensus 7 ~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~ 38 (212)
T cd07028 7 EADKDNVDFILSGVDLAMANALRRVMIAEVPT 38 (212)
T ss_pred EcCCCEEEEEEEccChhHHHHHHHHHHHcCcc
Confidence 35788999999999999999999888875 54
No 21
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=92.31 E-value=0.21 Score=38.16 Aligned_cols=39 Identities=23% Similarity=0.330 Sum_probs=30.3
Q ss_pred CCCCeeEEEE----ecCCcchHHHHHHHHhcC-CCeeeeeecCC
Q 033968 7 GDQSNATFSL----TEEDHTLANAVRFTLNQD-PRVTFCGYSIP 45 (107)
Q Consensus 7 ~~~n~~~~~i----~~EDHTLgNlLr~~L~~~-~~V~fAgY~vp 45 (107)
.+++.+.|.| .|.++|+||+||-.|+.. |+.-+-+-+|.
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 4568899999 779999999999888875 66655555544
No 22
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=92.22 E-value=0.35 Score=39.46 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=39.0
Q ss_pred eeeeeecCCCC-----CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 37 VTFCGYSIPHP-----SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 37 V~fAgY~vpHP-----le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
|.-+.|.|..- ...++.|-|.|+|. +|.+||..|++.|...+..+.+
T Consensus 171 V~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~ 223 (327)
T CHL00013 171 VRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH 223 (327)
T ss_pred eeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 66677777641 25689999999999 9999999999999999988754
No 23
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=91.87 E-value=0.17 Score=39.15 Aligned_cols=28 Identities=29% Similarity=0.345 Sum_probs=24.7
Q ss_pred CCCCeeEEEEecCCcchHHHHHHHHhcC
Q 033968 7 GDQSNATFSLTEEDHTLANAVRFTLNQD 34 (107)
Q Consensus 7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~ 34 (107)
.+++.+.|.+.|-++|+||+||-.|+..
T Consensus 8 ~~~~~~~f~~~g~~~s~~NalRRills~ 35 (259)
T cd07030 8 LDDDRARFVLEGVPPAFANAIRRAIISE 35 (259)
T ss_pred cCCCEEEEEEeCCCHHHHHHHHHHHHhc
Confidence 4568899999999999999999888875
No 24
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=90.56 E-value=0.32 Score=37.11 Aligned_cols=36 Identities=17% Similarity=0.184 Sum_probs=29.5
Q ss_pred CCCCCCeeEEEEecCCcchHHHHHHHHhcC-CCeeeee
Q 033968 5 AFGDQSNATFSLTEEDHTLANAVRFTLNQD-PRVTFCG 41 (107)
Q Consensus 5 ~~~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAg 41 (107)
++++++.++|.+. -+.|+||+||-.|+.. |+.-.-+
T Consensus 9 ~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~ 45 (195)
T PRK14979 9 KTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIEN 45 (195)
T ss_pred eccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEE
Confidence 5788999999999 9999999999888875 6544433
No 25
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=89.78 E-value=0.45 Score=36.42 Aligned_cols=33 Identities=36% Similarity=0.387 Sum_probs=25.9
Q ss_pred eEEEEecCCcchHHHHHHHHhcC-CCeeeeeecC
Q 033968 12 ATFSLTEEDHTLANAVRFTLNQD-PRVTFCGYSI 44 (107)
Q Consensus 12 ~~~~i~~EDHTLgNlLr~~L~~~-~~V~fAgY~v 44 (107)
+.|.+.+-++|+||+||-.|+.. |..-.-+.+|
T Consensus 2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I 35 (224)
T smart00662 2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI 35 (224)
T ss_pred eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence 67999999999999999888874 6655544443
No 26
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=89.18 E-value=0.59 Score=37.71 Aligned_cols=38 Identities=29% Similarity=0.339 Sum_probs=30.7
Q ss_pred CCCeeEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeecCC
Q 033968 8 DQSNATFSLT----EEDHTLANAVRFTLNQD-PRVTFCGYSIP 45 (107)
Q Consensus 8 ~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAgY~vp 45 (107)
+++.+.|.|. |.++|+||+||-.|+.. |+.-.-+-+|.
T Consensus 17 ~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~ 59 (310)
T PRK05182 17 DDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID 59 (310)
T ss_pred CCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc
Confidence 4688999996 99999999999888874 76666666653
No 27
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=88.89 E-value=1.2 Score=34.62 Aligned_cols=40 Identities=15% Similarity=0.320 Sum_probs=36.0
Q ss_pred CCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 48 SDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAK 87 (107)
Q Consensus 48 le~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~ 87 (107)
..++..+.|.|.|. +|.++++.|++-|++.++.|.+..+.
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 46678889999999 99999999999999999999988765
No 28
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=85.51 E-value=0.9 Score=35.81 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=26.5
Q ss_pred CCCCeeEEEEecCCcchHHHHHHHHhcC-CCee
Q 033968 7 GDQSNATFSLTEEDHTLANAVRFTLNQD-PRVT 38 (107)
Q Consensus 7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~V~ 38 (107)
.+++.++|.+.+=|+|+||+||-.|+.. |..-
T Consensus 8 ~~~~~~~F~l~~~~~s~aNALRRillsevPt~A 40 (265)
T cd07031 8 LTDDKVKFILENTDLSVANSLRRVMIAEVPTLA 40 (265)
T ss_pred cCCCEEEEEEEcCcHHHHHHHHHHHHHcCccce
Confidence 4568899999999999999999888774 5433
No 29
>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=84.75 E-value=2.3 Score=32.86 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=31.9
Q ss_pred CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 033968 49 DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRST 84 (107)
Q Consensus 49 e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~ 84 (107)
.+...+.|.|.|. +|.++|++|+.-|.+.++.|.++
T Consensus 222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~ 258 (259)
T cd07030 222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258 (259)
T ss_pred CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4567788999999 99999999999999999998765
No 30
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=84.18 E-value=0.96 Score=36.74 Aligned_cols=29 Identities=24% Similarity=0.055 Sum_probs=24.6
Q ss_pred CCCeeEEEEecCCcchHHHHHHHHhcC-CC
Q 033968 8 DQSNATFSLTEEDHTLANAVRFTLNQD-PR 36 (107)
Q Consensus 8 ~~n~~~~~i~~EDHTLgNlLr~~L~~~-~~ 36 (107)
..-.++|.+.|-+|||||+||-.|+.. |+
T Consensus 17 ~~~~ieplerG~g~tlgNALRRvLLSsiPg 46 (317)
T COG0202 17 AKFVIEPLERGFGVTLGNALRRVLLSSIPG 46 (317)
T ss_pred ccEEEEEeeeCCcchhHHHHHHHHHHcCcc
Confidence 466789999999999999999888874 54
No 31
>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=83.53 E-value=2.9 Score=33.65 Aligned_cols=37 Identities=16% Similarity=0.319 Sum_probs=33.1
Q ss_pred CCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHH
Q 033968 47 PSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 47 Ple~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~ 83 (107)
+-.+.+.+.|.+.|. +|.+.+.+|++-|.+.|+.+.+
T Consensus 253 ~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~ 290 (291)
T cd07032 253 RVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred EeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 346678999999999 9999999999999999998875
No 32
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=83.12 E-value=1 Score=36.80 Aligned_cols=40 Identities=18% Similarity=0.129 Sum_probs=30.3
Q ss_pred CCCCeeEEEEe----cCCcchHHHHHHHHhcC-CCeeeeeecCCC
Q 033968 7 GDQSNATFSLT----EEDHTLANAVRFTLNQD-PRVTFCGYSIPH 46 (107)
Q Consensus 7 ~~~n~~~~~i~----~EDHTLgNlLr~~L~~~-~~V~fAgY~vpH 46 (107)
..++.+.|.|. |..|||||+||-.|+.. |+.-+.+-+|.+
T Consensus 17 ~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 17 KRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred CCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 34566777775 57789999999888875 877777776654
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=79.16 E-value=1.6 Score=35.03 Aligned_cols=29 Identities=28% Similarity=0.252 Sum_probs=22.8
Q ss_pred ecCCcchHHHHHHHHhcC-CCeeeeeecCC
Q 033968 17 TEEDHTLANAVRFTLNQD-PRVTFCGYSIP 45 (107)
Q Consensus 17 ~~EDHTLgNlLr~~L~~~-~~V~fAgY~vp 45 (107)
.|.++||||+||-.|+.+ |++-..+-+|.
T Consensus 11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~ 40 (297)
T TIGR02027 11 RGFGITLGNALRRVLLSSIPGAAITAVKID 40 (297)
T ss_pred CCchhHHHHHHHHHHHhcCCceEEEEEEEc
Confidence 478899999999888875 77766666654
No 34
>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=71.51 E-value=21 Score=22.17 Aligned_cols=67 Identities=13% Similarity=0.121 Sum_probs=37.3
Q ss_pred eeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCC-CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHH
Q 033968 11 NATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPS-DARVNIRVQTTGD-PAREVLKDSCQELMLMCR 79 (107)
Q Consensus 11 ~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl-e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~ 79 (107)
++.|++.++-=+|..+|...-..+=++.-- -.-|++- ...+.++|.+++. + .+.++++++.|...+.
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 455666554444554444333333333222 1233332 4568889999876 3 3778888888877554
No 35
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=67.95 E-value=3.3 Score=34.40 Aligned_cols=23 Identities=39% Similarity=0.683 Sum_probs=21.3
Q ss_pred CCcchHHHHHHHHhcCCCeeeee
Q 033968 19 EDHTLANAVRFTLNQDPRVTFCG 41 (107)
Q Consensus 19 EDHTLgNlLr~~L~~~~~V~fAg 41 (107)
-.|++.|+||..|.+||+|.+.|
T Consensus 183 dT~sF~~aLraALReDPDVIlvG 205 (353)
T COG2805 183 DTLSFANALRAALREDPDVILVG 205 (353)
T ss_pred cHHHHHHHHHHHhhcCCCEEEEe
Confidence 45899999999999999999998
No 36
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=63.19 E-value=7.7 Score=27.50 Aligned_cols=37 Identities=11% Similarity=0.029 Sum_probs=28.9
Q ss_pred CCeeEEEEecCCcchHHHHHHHHhcCCC--eeeeeecCC
Q 033968 9 QSNATFSLTEEDHTLANAVRFTLNQDPR--VTFCGYSIP 45 (107)
Q Consensus 9 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~--V~fAgY~vp 45 (107)
+..+..++.+|.|.+|..+-..+++..+ |.+-|..+|
T Consensus 4 ~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp 42 (137)
T PRK02261 4 KTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTS 42 (137)
T ss_pred CEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCC
Confidence 4567889999999999999999999864 455555554
No 37
>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=61.04 E-value=10 Score=28.24 Aligned_cols=40 Identities=13% Similarity=0.062 Sum_probs=31.9
Q ss_pred CCCeeEEEEecCCcchHHHHHHHHhcCC--CeeeeeecCCCC
Q 033968 8 DQSNATFSLTEEDHTLANAVRFTLNQDP--RVTFCGYSIPHP 47 (107)
Q Consensus 8 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~--~V~fAgY~vpHP 47 (107)
.+..+-.++.||.|.||..+-..+++.. +|.|.|-.+|-.
T Consensus 84 ~~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e 125 (197)
T TIGR02370 84 LGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPID 125 (197)
T ss_pred CCeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHH
Confidence 4566889999999999999999999886 466667666643
No 38
>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=60.16 E-value=26 Score=25.93 Aligned_cols=40 Identities=13% Similarity=0.125 Sum_probs=30.6
Q ss_pred CCCeeEEEEecCCcchHHHHHHHHhcCC--CeeeeeecCCCC
Q 033968 8 DQSNATFSLTEEDHTLANAVRFTLNQDP--RVTFCGYSIPHP 47 (107)
Q Consensus 8 ~~n~~~~~i~~EDHTLgNlLr~~L~~~~--~V~fAgY~vpHP 47 (107)
.+..+..++.||.|+||..+-..+++.. +|.+.|-.+|..
T Consensus 82 ~~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~ 123 (201)
T cd02070 82 KGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPE 123 (201)
T ss_pred CCeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHH
Confidence 3456778999999999998888888876 455667666655
No 39
>PF10824 DUF2580: Protein of unknown function (DUF2580); InterPro: IPR022536 This entry represents the ESX-1 secretion-associated protein EspC protein family.
Probab=58.56 E-value=43 Score=20.94 Aligned_cols=42 Identities=14% Similarity=0.230 Sum_probs=32.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccc
Q 033968 62 PAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMKI 103 (107)
Q Consensus 62 ~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~~~~~~~ 103 (107)
.....+..++..+...+..+-+.+..+...|...++..+..+
T Consensus 57 ~~~~~~~~~~~~~~~~~~~~a~~L~~aA~~Y~~~D~~~a~~l 98 (100)
T PF10824_consen 57 EALEARQAALEQLAEALDEFADALRAAADRYEATDEDNAARL 98 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 345667778888888889999999999999998887654443
No 40
>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=56.53 E-value=48 Score=21.58 Aligned_cols=36 Identities=14% Similarity=0.255 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033968 62 PAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97 (107)
Q Consensus 62 ~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~ 97 (107)
+|.++|...+..|.+++.++.-.+..--..|+..+.
T Consensus 10 ~p~~~Ls~vl~~LqDE~~hm~~e~~~L~~~~~~~d~ 45 (79)
T PF06657_consen 10 SPGEALSEVLKALQDEFGHMKMEHQELQDEYKQMDP 45 (79)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 899999999999999999999999988555555443
No 41
>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=56.13 E-value=30 Score=23.47 Aligned_cols=27 Identities=11% Similarity=-0.039 Sum_probs=23.0
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCCee
Q 033968 12 ATFSLTEEDHTLANAVRFTLNQDPRVT 38 (107)
Q Consensus 12 ~~~~i~~EDHTLgNlLr~~L~~~~~V~ 38 (107)
+.+++.+|.|.+|..+-..+++..+.+
T Consensus 3 v~~~~~gd~H~lG~~~~~~~l~~~G~~ 29 (122)
T cd02071 3 LVAKPGLDGHDRGAKVIARALRDAGFE 29 (122)
T ss_pred EEEecCCChhHHHHHHHHHHHHHCCCE
Confidence 567889999999999999999987533
No 42
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=55.10 E-value=14 Score=28.05 Aligned_cols=41 Identities=10% Similarity=0.092 Sum_probs=32.1
Q ss_pred CCCCeeEEEEecCCcchHHHHHHHHhcCC--CeeeeeecCCCC
Q 033968 7 GDQSNATFSLTEEDHTLANAVRFTLNQDP--RVTFCGYSIPHP 47 (107)
Q Consensus 7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~~--~V~fAgY~vpHP 47 (107)
..+..+..++.||.|.||..|...+++.. +|.+-|-++|-+
T Consensus 87 ~~~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e 129 (213)
T cd02069 87 SKGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIE 129 (213)
T ss_pred CCCeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHH
Confidence 34566888999999999999999999886 566666666644
No 43
>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=52.36 E-value=40 Score=22.32 Aligned_cols=26 Identities=8% Similarity=0.146 Sum_probs=21.7
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCCe
Q 033968 12 ATFSLTEEDHTLANAVRFTLNQDPRV 37 (107)
Q Consensus 12 ~~~~i~~EDHTLgNlLr~~L~~~~~V 37 (107)
+...+.+|.|+||..+-..+++..+.
T Consensus 3 l~~~~~~e~H~lG~~~~~~~l~~~G~ 28 (119)
T cd02067 3 VIATVGGDGHDIGKNIVARALRDAGF 28 (119)
T ss_pred EEEeeCCchhhHHHHHHHHHHHHCCC
Confidence 45778999999999999998887653
No 44
>PRK00549 competence damage-inducible protein A; Provisional
Probab=49.89 E-value=86 Score=26.14 Aligned_cols=39 Identities=21% Similarity=0.381 Sum_probs=28.2
Q ss_pred cchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCH
Q 033968 21 HTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPA 63 (107)
Q Consensus 21 HTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p 63 (107)
=.|...|...+...++|.++.| |+ .+.+.+|+...+.+.
T Consensus 191 s~l~~~L~~l~~~~~~v~ig~~--~~--~~~~~vrl~~~~~~~ 229 (414)
T PRK00549 191 SQLATTLRDLIDNQTNPTIAPY--AK--DGEVTLRLTAKARSE 229 (414)
T ss_pred HHHHHHHHHHHhcCCCCEEEEC--cc--CCEEEEEEEEecCCH
Confidence 4577788777778899998866 33 356788888776543
No 45
>KOG2972 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.02 E-value=44 Score=27.00 Aligned_cols=52 Identities=17% Similarity=0.252 Sum_probs=39.6
Q ss_pred chHHHHHHHHhc-CCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHH
Q 033968 22 TLANAVRFTLNQ-DPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQE 73 (107)
Q Consensus 22 TLgNlLr~~L~~-~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~ 73 (107)
++-|.|+...-+ -|.|.|+-|.+-||.-=-+++..-|+.. ....+++.++++
T Consensus 93 ~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~nk 146 (276)
T KOG2972|consen 93 GIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIFNK 146 (276)
T ss_pred HHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHHHH
Confidence 677888888776 4899999999999998888888888765 444455544443
No 46
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=48.30 E-value=61 Score=19.67 Aligned_cols=67 Identities=21% Similarity=0.174 Sum_probs=36.9
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCC-CCceeEEEEeCCCCHHHHHHHHHHHHHHHHH
Q 033968 12 ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPS-DARVNIRVQTTGDPAREVLKDSCQELMLMCR 79 (107)
Q Consensus 12 ~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPl-e~~i~lrIqT~~~~p~eal~~Al~~L~~~~~ 79 (107)
+.|++.++-=+|.++|...-...=++.-- ...|-+. .....+.|...+..-...++++++.|.+.|.
T Consensus 2 l~~~l~d~pG~L~~vL~~f~~~~vni~~I-~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~~~~ 69 (75)
T cd04880 2 LVFSLKNKPGALAKALKVFAERGINLTKI-ESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKRVTE 69 (75)
T ss_pred EEEEeCCcCCHHHHHHHHHHHCCCCEEEE-EeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHHhCC
Confidence 45677666666777777665555454444 3334333 3445666666553112556666666665543
No 47
>PLN02231 alanine transaminase
Probab=47.28 E-value=83 Score=26.98 Aligned_cols=58 Identities=10% Similarity=0.003 Sum_probs=38.9
Q ss_pred HHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 27 VRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFA 86 (107)
Q Consensus 27 Lr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f~ 86 (107)
+...|++..+|.+.--..-.+..+.-.||+.. ..+.+.|++|+++|...+..+.++|+
T Consensus 476 ~~~~Ll~~~GV~vvPGs~Fg~~~g~~~~Rit~--~~~~e~l~eal~RL~~~~~~~~~~~~ 533 (534)
T PLN02231 476 YCKRLLNATGIVVVPGSGFGQVPGTWHFRCTI--LPQEDKIPAIVSRLTEFHKSFMDEFR 533 (534)
T ss_pred HHHHHHHhcCEEEeCCcccCCCCCCCeEEEEe--CCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44556666666655333223334455677764 35779999999999998888877764
No 48
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=42.86 E-value=52 Score=26.59 Aligned_cols=66 Identities=17% Similarity=0.211 Sum_probs=50.7
Q ss_pred HHHHHHHh--------cCCCeeeeeecCCC----CC-----CCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 25 NAVRFTLN--------QDPRVTFCGYSIPH----PS-----DARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFA 86 (107)
Q Consensus 25 NlLr~~L~--------~~~~V~fAgY~vpH----Pl-----e~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~ 86 (107)
|.||+.+. .-|.+..++|.-+- |. -+++++.|...|+ .|.+++..|+.-|.+.+..|.....
T Consensus 187 n~lrhT~y~~e~~~~~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~ 266 (285)
T KOG1522|consen 187 NKLRHTLYWFEEDDLIEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALS 266 (285)
T ss_pred HhhhccCCCccccchhhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 77776655 34667788877651 11 2578999999988 9999999999999999999888776
Q ss_pred HHHH
Q 033968 87 KAVD 90 (107)
Q Consensus 87 ~a~~ 90 (107)
...+
T Consensus 267 ~~~q 270 (285)
T KOG1522|consen 267 TEDQ 270 (285)
T ss_pred ccch
Confidence 6554
No 49
>COG1027 AspA Aspartate ammonia-lyase [Amino acid transport and metabolism]
Probab=42.34 E-value=62 Score=27.90 Aligned_cols=67 Identities=22% Similarity=0.334 Sum_probs=46.4
Q ss_pred hHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033968 23 LANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD---PAREVLKDSCQELMLMCRHVRSTFAKAVDDFRT 94 (107)
Q Consensus 23 LgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~---~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~ 94 (107)
+.|.=-+.|-..++ -|.+-||.+ .+++-=.|++. -..-++-..+..|+..++.|.+.|+...++|+.
T Consensus 112 IAN~AlE~lG~~KG----eY~~~hPnd-hVNmsQSTND~yPTa~ria~~~~l~~L~~al~~L~~af~~Ka~EF~~ 181 (471)
T COG1027 112 IANRALELLGHEKG----EYQYLHPND-HVNMSQSTNDAYPTAFRIAVYKSLRKLIDALEDLIEAFERKAKEFAD 181 (471)
T ss_pred HHHHHHHHhcCCCC----ceeeeCCcc-ccchhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44544444444443 499999966 45555555554 234577788889999999999999998888864
No 50
>PF12909 DUF3832: Protein of unknown function (DUF3832); InterPro: IPR024308 This domain found in bacteria and Acanthamoeba polyphaga mimivirus (APMV) L591 protein has no known function. In Q0AZ30 from SWISSPROT and other uncharacterised proteins this domain is found C-terminal, while the N terminus shows remote homology to the bacterial toxin/antitoxin 'addiction module' (PF12910 from PFAM).; PDB: 3K6Q_C.
Probab=39.49 E-value=59 Score=21.87 Aligned_cols=34 Identities=15% Similarity=0.202 Sum_probs=28.2
Q ss_pred EEeCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 56 VQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAV 89 (107)
Q Consensus 56 IqT~~~~p~eal~~Al~~L~~~~~~l~~~f~~a~ 89 (107)
|-++|.+..+|+.+.++.|++.++...+.|.--.
T Consensus 28 i~~~g~T~eeA~~~lie~l~dYAedy~~~~~~~~ 61 (89)
T PF12909_consen 28 IYANGPTLEEAIEDLIEDLRDYAEDYMNRFPLFY 61 (89)
T ss_dssp EEEEESSHHHHHHHHHHHHHHHHHHHHHTHHHHH
T ss_pred EEecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5566679999999999999999999998885443
No 51
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=38.37 E-value=80 Score=22.73 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=11.3
Q ss_pred hcCCCeeeeeecCCCCCCC
Q 033968 32 NQDPRVTFCGYSIPHPSDA 50 (107)
Q Consensus 32 ~~~~~V~fAgY~vpHPle~ 50 (107)
++.-+..+.||+ ||||.+
T Consensus 10 ~~~~~~~~~~~~-~~~~~~ 27 (127)
T PRK12729 10 WRIYNSGYSGNK-PHPLSP 27 (127)
T ss_pred HHHHhcccCCCC-CCCCCC
Confidence 344444566665 999865
No 52
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=37.32 E-value=1.4e+02 Score=22.49 Aligned_cols=37 Identities=8% Similarity=0.254 Sum_probs=31.6
Q ss_pred eCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033968 58 TTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRT 94 (107)
Q Consensus 58 T~~~~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~ 94 (107)
.+.+.....+.+++.......+.+.+....-++.|+.
T Consensus 120 ~~~~~ir~~I~~~i~~~~~~~~eid~~Vr~ki~~y~r 156 (183)
T PF04368_consen 120 VSENRIRNIIFKSIEEYLKEEEEIDDEVREKIKSYKR 156 (183)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 3344677899999999999999999999999999887
No 53
>PTZ00377 alanine aminotransferase; Provisional
Probab=36.96 E-value=1.6e+02 Score=24.38 Aligned_cols=57 Identities=9% Similarity=0.112 Sum_probs=36.8
Q ss_pred HHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 27 VRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTF 85 (107)
Q Consensus 27 Lr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f 85 (107)
+...+++..+|.+.-...-.+....-.|||-.. .+.+-+++|+++|.+.+..+.++|
T Consensus 424 ~~~~ll~~~gV~v~pG~~F~~~~~~~~~Rls~~--~~~e~l~~~l~rl~~~~~~~~~~~ 480 (481)
T PTZ00377 424 YCLELLESTGIVVVPGSGFGQKPGTYHFRITIL--PPEEQIEEMVKKIKEFHESFMKKY 480 (481)
T ss_pred HHHHHHHHcCEEEeCCcccCCCCCCCEEEEEEC--CCHHHHHHHHHHHHHHHHHHHHhh
Confidence 334566666776653332222223346888764 456889999999999888777765
No 54
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=36.36 E-value=1.3e+02 Score=22.57 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033968 60 GDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97 (107)
Q Consensus 60 ~~~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~ 97 (107)
.+..+..++.-+..|++....++.++..-+..-+.+..
T Consensus 38 ~~~avSL~erQ~~~LR~~~~~L~~~l~~Li~~Ar~Ne~ 75 (225)
T PF04340_consen 38 SGGAVSLVERQLERLRERNRQLEEQLEELIENARENEA 75 (225)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34688999999999999999999999998877776665
No 55
>KOG0758 consensus Mitochondrial carnitine-acylcarnitine carrier protein [Energy production and conversion]
Probab=36.20 E-value=42 Score=27.40 Aligned_cols=32 Identities=28% Similarity=0.498 Sum_probs=23.0
Q ss_pred eeecCCCCCCCceeEEEEeCCCCH----HHHHHHHHH
Q 033968 40 CGYSIPHPSDARVNIRVQTTGDPA----REVLKDSCQ 72 (107)
Q Consensus 40 AgY~vpHPle~~i~lrIqT~~~~p----~eal~~Al~ 72 (107)
|+--|-||++ .+.+|+||-..+. ++++++.+.
T Consensus 26 ~~vlVGhPfD-TvKVRlQt~~~~~y~~~~~c~~~t~~ 61 (297)
T KOG0758|consen 26 AQVLVGHPFD-TVKVRLQTQNTPVYKGTLDCVKKTLK 61 (297)
T ss_pred hhhhccCCcc-ceEEeeeccCCCCcccHHHHHHHHHH
Confidence 5667899986 7899999976533 566655543
No 56
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=36.19 E-value=2e+02 Score=22.01 Aligned_cols=81 Identities=14% Similarity=0.189 Sum_probs=53.7
Q ss_pred ecCCcchHHHHHHHHhcCCCeeeee---------------------------ecCCCCCCCceeEEEEeCCC-CHHH---
Q 033968 17 TEEDHTLANAVRFTLNQDPRVTFCG---------------------------YSIPHPSDARVNIRVQTTGD-PARE--- 65 (107)
Q Consensus 17 ~~EDHTLgNlLr~~L~~~~~V~fAg---------------------------Y~vpHPle~~i~lrIqT~~~-~p~e--- 65 (107)
.+|||==.|-|-+.|-++-+|.-|- |.-.-|.-++++..|..+-. +|.+
T Consensus 72 q~~d~Y~~nGlL~mLdRNrrvK~aPe~wq~~~~~fd~ViTCEERcfdaicEdly~rg~~ln~~v~~iNvDIkD~~e~A~~ 151 (197)
T COG5211 72 QNEDHYRENGLLYMLDRNRRVKEAPENWQQRSEDFDLVITCEERCFDAICEDLYARGPSLNQCVFMINVDIKDTPEDAIA 151 (197)
T ss_pred hhhhhhhhccHHHHHHhcchhhhCchhhhhccccccEEEEehHHHHHHHHHHHHhcCccccccEEEEEeeccCChhhhhh
Confidence 4567777777777777776655332 33345666677776766543 4544
Q ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033968 66 ---VLKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97 (107)
Q Consensus 66 ---al~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~ 97 (107)
|+.+-++.|.+.-+.|+..|...+.+|+++..
T Consensus 152 G~kaILelvd~L~~~~e~lE~~~~sil~~~qsnh~ 186 (197)
T COG5211 152 GAKAILELVDVLAKEEERLEYAVDSILRRYQSNHK 186 (197)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 44455566777778888888889999998654
No 57
>cd01406 SIR2-like Sir2-like: Prokaryotic group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines; and are members of the SIR2 superfamily of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation.
Probab=35.89 E-value=44 Score=25.01 Aligned_cols=42 Identities=26% Similarity=0.473 Sum_probs=29.6
Q ss_pred CCCCCCCCeeEEEEecCCc--------chHHHHHHHHhcCCCeeeeeecCCCC
Q 033968 3 HGAFGDQSNATFSLTEEDH--------TLANAVRFTLNQDPRVTFCGYSIPHP 47 (107)
Q Consensus 3 ~~~~~~~n~~~~~i~~EDH--------TLgNlLr~~L~~~~~V~fAgY~vpHP 47 (107)
||.-..+.++.|+ .+|. .+.+.|+..+. ..-|.|.||...-|
T Consensus 143 HG~~~~~~~~VlT--~~dY~~~~~~~~~~~~~l~~ll~-~~~~LFiG~S~~D~ 192 (242)
T cd01406 143 HGDVDDDESIVLT--KSDYERYYLKNGWATKFLKSDLE-KYTVLFIGYSLTDP 192 (242)
T ss_pred ecccCCCCceEec--HHHHHHHHhccHHHHHHHHHHHh-cCcEEEEEcCCCCC
Confidence 7888888776444 3343 45677776666 56799999997766
No 58
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=35.88 E-value=1.2e+02 Score=19.29 Aligned_cols=33 Identities=12% Similarity=0.114 Sum_probs=22.8
Q ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 53 NIRVQTTGDPAREVLKDSCQELMLMCRHVRSTF 85 (107)
Q Consensus 53 ~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f 85 (107)
.|++...+.++..|+..|++.|...+...++..
T Consensus 60 ~l~a~~~~~d~~~Aid~a~~klerql~k~k~k~ 92 (95)
T TIGR00741 60 VIRASAEHEDMYAAIDLAIDKLERQLRKLKEKR 92 (95)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHHHHHHHhhh
Confidence 345554455888999988888877776665543
No 59
>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=35.58 E-value=1.2e+02 Score=19.21 Aligned_cols=31 Identities=6% Similarity=0.155 Sum_probs=22.4
Q ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHHHHHHH
Q 033968 53 NIRVQTTGDPAREVLKDSCQELMLMCRHVRS 83 (107)
Q Consensus 53 ~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~ 83 (107)
.|++...+.+...|+..|++.|...+...++
T Consensus 62 ~l~a~~~~~d~~~Aid~a~dkl~rql~k~k~ 92 (97)
T PF02482_consen 62 VLVAEESAEDLYAAIDEAFDKLERQLRKYKE 92 (97)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHHHHHHHH
T ss_pred eEEEEEecCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555558999999999888877766554
No 60
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=34.85 E-value=1.3e+02 Score=19.44 Aligned_cols=33 Identities=9% Similarity=0.157 Sum_probs=22.4
Q ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 53 NIRVQTTGDPAREVLKDSCQELMLMCRHVRSTF 85 (107)
Q Consensus 53 ~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f 85 (107)
.|+++..+.++..|+..|++.|...+...++.+
T Consensus 60 ~l~a~~~~~d~y~Aid~a~~klerqL~k~k~k~ 92 (95)
T PRK10470 60 EIHASAEGQDMYAAIDGLIDKLARQLTKHKDKL 92 (95)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455665556888888888877776666555543
No 61
>PF12179 IKKbetaNEMObind: I-kappa-kinase-beta NEMO binding domain; InterPro: IPR022007 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with PF00069 from PFAM. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO. ; GO: 0008384 IkappaB kinase activity; PDB: 3BRT_C 3BRV_C.
Probab=34.45 E-value=96 Score=17.92 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhcccc
Q 033968 73 ELMLMCRHVRSTFAKAVDDFRTSEKVQAMKID 104 (107)
Q Consensus 73 ~L~~~~~~l~~~f~~a~~~~~~~~~~~~~~~~ 104 (107)
.|+.+-..+..++..+++...+.++.|.|.-|
T Consensus 3 ~lv~En~~~lsqL~s~mqdt~~Eq~~S~m~lD 34 (38)
T PF12179_consen 3 QLVEENQNYLSQLESLMQDTMKEQDSSFMSLD 34 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCCS-GGGS-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcchHHhcc
Confidence 45555555666666666666666666677655
No 62
>PRK01215 competence damage-inducible protein A; Provisional
Probab=34.09 E-value=2.3e+02 Score=22.20 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=28.6
Q ss_pred EEEEecCC-cchHHHHHHHHhcCCCeee--e--eecCCCCCCCceeEEEEeCCC
Q 033968 13 TFSLTEED-HTLANAVRFTLNQDPRVTF--C--GYSIPHPSDARVNIRVQTTGD 61 (107)
Q Consensus 13 ~~~i~~ED-HTLgNlLr~~L~~~~~V~f--A--gY~vpHPle~~i~lrIqT~~~ 61 (107)
++.+.|-+ =+|.-.|...+.+.|+|.+ + ||. +|+ +.+.|||..++.
T Consensus 183 ~~~~~Gi~Es~l~~~l~~l~~~~~~~~~~s~p~~~~-~~~--~~v~vrl~~~~~ 233 (264)
T PRK01215 183 SILVEGVMESDLAPYVKELVKKYDRVYVKSHPKGYE-VSK--PILEIQIAGSGE 233 (264)
T ss_pred EEEECCCCHHHHHHHHHHHHHhCCCCEEecCcccee-cCC--CeEEEEEEEecC
Confidence 34454433 3566677777777889988 4 344 343 567788876654
No 63
>PRK00407 hypothetical protein; Provisional
Probab=33.68 E-value=75 Score=22.59 Aligned_cols=34 Identities=18% Similarity=0.410 Sum_probs=23.1
Q ss_pred eec-CCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHH
Q 033968 41 GYS-IPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMC 78 (107)
Q Consensus 41 gY~-vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~ 78 (107)
+|+ ++|+-+ +.|...|.++.+++.+|+..+.+.+
T Consensus 3 ~ye~ldHtAD----v~i~~~g~tleE~F~~aa~a~~~~m 37 (139)
T PRK00407 3 SYEFFEHTAD----IGIRAYGRTLEEAFENAALAVFDVI 37 (139)
T ss_pred CeeEcCcchh----EEEEEEECCHHHHHHHHHHHHHHhh
Confidence 455 678755 4455556688888888888766554
No 64
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=33.13 E-value=1.3e+02 Score=22.72 Aligned_cols=34 Identities=18% Similarity=0.281 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033968 64 REVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97 (107)
Q Consensus 64 ~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~ 97 (107)
-++|..-+..+....+.|.+.|..++...+...+
T Consensus 109 ~evL~qr~~kle~ErdeL~~kf~~~i~evqQk~~ 142 (201)
T PF13851_consen 109 HEVLEQRFEKLEQERDELYRKFESAIQEVQQKTG 142 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3788888999999999999999999988887665
No 65
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=32.81 E-value=37 Score=29.55 Aligned_cols=24 Identities=42% Similarity=0.555 Sum_probs=21.9
Q ss_pred cCCcchHHHHHHHHhcCCCeeeee
Q 033968 18 EEDHTLANAVRFTLNQDPRVTFCG 41 (107)
Q Consensus 18 ~EDHTLgNlLr~~L~~~~~V~fAg 41 (107)
+-+-|..++||..|-+||+|.+.|
T Consensus 311 k~gltfa~~LRa~LRqDPDvImVG 334 (500)
T COG2804 311 KIGLTFARALRAILRQDPDVIMVG 334 (500)
T ss_pred ccCCCHHHHHHHHhccCCCeEEEe
Confidence 456899999999999999999988
No 66
>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=31.55 E-value=1.2e+02 Score=18.03 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 63 AREVLKDSCQELMLMCRHVRSTFAKAVDDFR 93 (107)
Q Consensus 63 p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~ 93 (107)
+-..|-..+..+.+.+.++++.++..+++-.
T Consensus 2 ~~~~l~~ql~~l~~~l~elk~~l~~Q~kE~~ 32 (45)
T PF11598_consen 2 VDSQLIKQLSELNQMLQELKELLRQQIKETR 32 (45)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788899999999999999998887644
No 67
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=31.39 E-value=34 Score=24.82 Aligned_cols=29 Identities=24% Similarity=0.521 Sum_probs=21.7
Q ss_pred HHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeC
Q 033968 26 AVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT 59 (107)
Q Consensus 26 lLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~ 59 (107)
.+=.+|.++|+|+|||..-. -.++||+-+
T Consensus 48 ~~yKqik~np~vefcg~~kd-----g~~vrlrg~ 76 (132)
T COG5015 48 PYYKQIKKNPEVEFCGMDKD-----GVMVRLRGR 76 (132)
T ss_pred HHHHHHhhCCCeEEEEecCC-----ceEEEEeee
Confidence 45678999999999998865 355666543
No 68
>COG0634 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=30.44 E-value=55 Score=24.86 Aligned_cols=20 Identities=10% Similarity=0.184 Sum_probs=16.8
Q ss_pred EecCCcchHHHHHHHHhcCC
Q 033968 16 LTEEDHTLANAVRFTLNQDP 35 (107)
Q Consensus 16 i~~EDHTLgNlLr~~L~~~~ 35 (107)
|-++.|||-.+.+....+.|
T Consensus 102 IiDsG~TLs~i~~~l~~r~a 121 (178)
T COG0634 102 IIDSGLTLSKVRDLLKERGA 121 (178)
T ss_pred ccccChhHHHHHHHHHhCCC
Confidence 55788999999999888865
No 69
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=30.40 E-value=97 Score=25.20 Aligned_cols=39 Identities=18% Similarity=0.144 Sum_probs=33.4
Q ss_pred CceeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 50 ARVNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAKA 88 (107)
Q Consensus 50 ~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~a 88 (107)
.+..+.+-|+|. .|.+|+..|.+-+.+.|..+.+.+...
T Consensus 188 Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~ 227 (317)
T COG0202 188 DHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKA 227 (317)
T ss_pred eeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 356677778888 999999999999999999999888764
No 70
>KOG0427 consensus Ubiquitin conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=30.20 E-value=1.4e+02 Score=22.02 Aligned_cols=49 Identities=18% Similarity=0.356 Sum_probs=37.6
Q ss_pred hcCCCeeeeeecCCCC---CCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHH
Q 033968 32 NQDPRVTFCGYSIPHP---SDARVNIRVQTTGDPAREVLKDSCQELMLMCRH 80 (107)
Q Consensus 32 ~~~~~V~fAgY~vpHP---le~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~ 80 (107)
+..|.|.|.|=.=-|| +...|-|.|-+++=+|.-.+...|-.|.+++..
T Consensus 75 ~esPqVmF~~~~P~HPHiYSNGHICL~iL~d~WsPAmsv~SvClSIlSMLSS 126 (161)
T KOG0427|consen 75 MESPQVMFVGPAPLHPHIYSNGHICLDILYDSWSPAMSVQSVCLSILSMLSS 126 (161)
T ss_pred CCCCeEEEecCCCCCCceecCCeEEEEeecccCCcchhhHHHHHHHHHHHcc
Confidence 5679999999843388 456788899887668877777777777777654
No 71
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=29.99 E-value=1.7e+02 Score=19.41 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC
Q 033968 24 ANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD 61 (107)
Q Consensus 24 gNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~ 61 (107)
...++..|...|+++..+..-+ .+++.+.|.+.+.
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~---~GKiVVtiE~~~~ 53 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAP---SGQLIVVVEAEDS 53 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCC---CCeEEEEEEeCCh
Confidence 4567889999999998876433 6799999997665
No 72
>COG2033 Desulfoferrodoxin [Energy production and conversion]
Probab=29.13 E-value=38 Score=24.39 Aligned_cols=12 Identities=42% Similarity=0.814 Sum_probs=9.5
Q ss_pred eeecCCCCCCCce
Q 033968 40 CGYSIPHPSDARV 52 (107)
Q Consensus 40 AgY~vpHPle~~i 52 (107)
.| .||||++++=
T Consensus 57 VG-~IpHPmt~eH 68 (126)
T COG2033 57 VG-EIPHPMTPEH 68 (126)
T ss_pred Ec-ccCCCCCCce
Confidence 45 8999998863
No 73
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=29.01 E-value=1.6e+02 Score=20.27 Aligned_cols=34 Identities=15% Similarity=0.223 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC
Q 033968 24 ANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD 61 (107)
Q Consensus 24 gNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~ 61 (107)
.+.++..|+..|+|+..+-.-+ .++++.|++++.
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~----GKlVVVie~~~~ 53 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE----GKLVVVIEAEDS 53 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC----ceEEEEEEcCch
Confidence 4678999999999998776543 799999998764
No 74
>TIGR01546 GAPDH-II_archae glyceraldehyde-3-phosphate dehydrogenase, type II. All of the members of the seed are characterized. See, for instance. This model is very solid, there are no species falling between trusted and noise at this time. The closest relatives scoring in the noise are the class I GAPDH's.
Probab=28.34 E-value=1.6e+02 Score=24.17 Aligned_cols=51 Identities=12% Similarity=0.144 Sum_probs=39.0
Q ss_pred cchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHH
Q 033968 21 HTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQE 73 (107)
Q Consensus 21 HTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~ 73 (107)
|| +-.+...|=.-+ +.=.+++||.|.-+-.-|.+++++....+-+.++++.
T Consensus 190 ~~-a~av~~VlP~L~-i~g~AvrVPt~~vs~~dl~v~l~~~~t~eeV~~~l~~ 240 (333)
T TIGR01546 190 HH-GPDVQTVIPNLN-IETMAFVVPTTLMHVHSIMVELKKPVTKDDIIDILEN 240 (333)
T ss_pred ch-HHHHHHcCCCCC-ccEEEEEeCCCCcEEEEEEEEECCCCCHHHHHHHHHh
Confidence 77 888888877666 7788899999999999999999877333444445543
No 75
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=27.99 E-value=1.3e+02 Score=18.86 Aligned_cols=23 Identities=9% Similarity=0.094 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Q 033968 60 GDPAREVLKDSCQELMLMCRHVR 82 (107)
Q Consensus 60 ~~~p~eal~~Al~~L~~~~~~l~ 82 (107)
+.+...|+..|++.|...+...+
T Consensus 69 ~~d~~~Aid~a~~kl~rqL~k~k 91 (93)
T cd00552 69 AEDLYAAIDLAVDKLERQLRKYK 91 (93)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhc
Confidence 33888899888888877665543
No 76
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=26.99 E-value=1.4e+02 Score=17.58 Aligned_cols=46 Identities=9% Similarity=-0.013 Sum_probs=27.8
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCC
Q 033968 12 ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTG 60 (107)
Q Consensus 12 ~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~ 60 (107)
+.+.+.++--.|..++.-.-..+=+|... |..++ .++..++++++.
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i-~~~~~--~~~~~~rl~~~~ 49 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRAL-SIADT--SEFGILRLIVSD 49 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEE-EEEec--CCCCEEEEEECC
Confidence 45566666666777666555555555544 44333 236899999844
No 77
>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=26.81 E-value=90 Score=20.73 Aligned_cols=30 Identities=17% Similarity=0.134 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 62 PAREVLKDSCQELMLMCRHVRSTFAKAVDD 91 (107)
Q Consensus 62 ~p~eal~~Al~~L~~~~~~l~~~f~~a~~~ 91 (107)
.|-..|.++|+.=-+-++.++++|.++...
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 577889999998888999999999987765
No 78
>COG4495 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.52 E-value=1.5e+02 Score=20.85 Aligned_cols=59 Identities=17% Similarity=0.141 Sum_probs=34.0
Q ss_pred HHHHhcCCCeeeeeec-CCCCCC---CceeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 28 RFTLNQDPRVTFCGYS-IPHPSD---ARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDD 91 (107)
Q Consensus 28 r~~L~~~~~V~fAgY~-vpHPle---~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f~~a~~~ 91 (107)
|.....+. =...+|. +|||-- +.-.+.++ +.+..+++.++..+=.+. .+.+++..|++.
T Consensus 29 R~~~k~~~-~~~fDY~a~~yP~G~~~~d~v~yFn--~e~I~eVv~~Gy~D~~e~--~~~eqL~qa~~~ 91 (109)
T COG4495 29 RGQIKVDE-ETMFDYSACPYPEGELSDDKVAYFN--HENIDEVVFEGYEDDDEA--LRFEQLKQAKKE 91 (109)
T ss_pred ccceeecc-eeeeccccccCCccccccceEEEec--ccchHHHHhhhcccchHH--HHHHHHHHHHhh
Confidence 33444444 3467777 899954 33334443 348999999998776553 333344444443
No 79
>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=26.02 E-value=80 Score=25.46 Aligned_cols=28 Identities=29% Similarity=0.315 Sum_probs=24.8
Q ss_pred CCCCeeEEEEecCCcchHHHHHHHHhcC
Q 033968 7 GDQSNATFSLTEEDHTLANAVRFTLNQD 34 (107)
Q Consensus 7 ~~~n~~~~~i~~EDHTLgNlLr~~L~~~ 34 (107)
.+++.++|.+.|-|=.+.|+||-.|+..
T Consensus 8 ~~~~~~~f~l~~~d~s~ANAlRRimiaE 35 (291)
T cd07032 8 LSDEELEFDLIGVDASIANAFRRILLAE 35 (291)
T ss_pred CCCCEEEEEEecCCHHHHHHHHHHHHhc
Confidence 4678999999999999999999887764
No 80
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=25.59 E-value=1.1e+02 Score=23.78 Aligned_cols=33 Identities=9% Similarity=-0.044 Sum_probs=19.4
Q ss_pred eeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHH
Q 033968 39 FCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMC 78 (107)
Q Consensus 39 fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~ 78 (107)
.++|-+||++.+. .+. ...+.+.+|++.+.+.+
T Consensus 5 v~~~~~~H~~~~~-------~~~~~~~~~~~~al~~~~~~l 38 (268)
T cd07367 5 VGAAATSHILMSP-------KGVEDQAARVVQGMAEIGRRV 38 (268)
T ss_pred EEEEecCCcCcCC-------CCchHHHHHHHHHHHHHHHHH
Confidence 5789999975542 333 44455555555555444
No 81
>PRK10963 hypothetical protein; Provisional
Probab=25.25 E-value=1.4e+02 Score=22.66 Aligned_cols=60 Identities=15% Similarity=0.118 Sum_probs=40.7
Q ss_pred HHHHHHhcCCCe------eeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033968 26 AVRFTLNQDPRV------TFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEK 97 (107)
Q Consensus 26 lLr~~L~~~~~V------~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~ 97 (107)
-++.+|..+|+- .++.-++|||- + ..+..++..++.|++....++.++..-+..-+.+..
T Consensus 7 ~V~~yL~~~PdFf~~h~~Ll~~L~lph~~-----------~-gaVSL~ErQ~~~LR~r~~~Le~~l~~Li~~A~~Ne~ 72 (223)
T PRK10963 7 AVVDYLLQNPDFFIRNARLVEQMRVPHPV-----------R-GTVSLVEWQMARQRNHIHVLEEEMTLLMEQAIANED 72 (223)
T ss_pred HHHHHHHHCchHHhhCHHHHHhccCCCCC-----------C-CeecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467778888762 12334566662 2 255677888888888888888888887776665554
No 82
>PRK15197 secreted effector protein PipB; Provisional
Probab=25.03 E-value=3.2e+02 Score=22.05 Aligned_cols=41 Identities=22% Similarity=0.242 Sum_probs=26.4
Q ss_pred eeeeeecC----CCC---CCCceeEEEEeCCC-CHHHHHHHHHHHHHHH
Q 033968 37 VTFCGYSI----PHP---SDARVNIRVQTTGD-PAREVLKDSCQELMLM 77 (107)
Q Consensus 37 V~fAgY~v----pHP---le~~i~lrIqT~~~-~p~eal~~Al~~L~~~ 77 (107)
+.|.||.| |-| ..+.+.+.|.-.|. -+.++..+.+..+...
T Consensus 84 ~~~~g~~~~fs~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~~r~ 132 (291)
T PRK15197 84 EDVNGCTICLSCGAASENTDPMVIIEVNKNGKTVTDKVDSERFWNVCRM 132 (291)
T ss_pred eecCCeEEEeccCCCcccCCceEEEEEecCCcchHHHHHHHHHHHHHHH
Confidence 78899998 333 34457777775555 5567777766555544
No 83
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=24.99 E-value=1.2e+02 Score=19.50 Aligned_cols=34 Identities=12% Similarity=0.172 Sum_probs=27.6
Q ss_pred HHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC
Q 033968 24 ANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD 61 (107)
Q Consensus 24 gNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~ 61 (107)
...++..|...|+|+..+-.-. +++.+.|.+.+.
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~----GKiVVtiE~~~~ 50 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED----GKIVVTIEAESS 50 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT----TEEEEEEEESSH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC----CeEEEEEEeCCh
Confidence 5678899999999998887643 899999998654
No 84
>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=24.32 E-value=1.5e+02 Score=22.35 Aligned_cols=33 Identities=18% Similarity=0.375 Sum_probs=25.5
Q ss_pred CCeeEEEEecCCcchHHHHHHHHhcCCCeeeee
Q 033968 9 QSNATFSLTEEDHTLANAVRFTLNQDPRVTFCG 41 (107)
Q Consensus 9 ~n~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAg 41 (107)
++...+.-....+++..+|+..|..+|++.+.|
T Consensus 172 ~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiig 204 (270)
T PF00437_consen 172 PNQIQIQTRRDEISYEDLLKSALRQDPDVIIIG 204 (270)
T ss_dssp SSEEEEEEETTTBSHHHHHHHHTTS--SEEEES
T ss_pred cceEEEEeecCcccHHHHHHHHhcCCCCccccc
Confidence 455565555688999999999999999999887
No 85
>KOG4014 consensus Uncharacterized conserved protein (contains TPR repeat) [Function unknown]
Probab=24.26 E-value=1.4e+02 Score=23.61 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 033968 69 DSCQELMLMCRHVRSTFAKAVDDFRTSEK 97 (107)
Q Consensus 69 ~Al~~L~~~~~~l~~~f~~a~~~~~~~~~ 97 (107)
++|..|-+.++-|++.|++|++-|+.+=.
T Consensus 35 e~C~lLgdYlEgi~knF~~A~kv~K~nCd 63 (248)
T KOG4014|consen 35 ESCQLLGDYLEGIQKNFQAAVKVFKKNCD 63 (248)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 68999999999999999999999887543
No 86
>COG4115 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.16 E-value=68 Score=21.62 Aligned_cols=24 Identities=29% Similarity=0.553 Sum_probs=19.0
Q ss_pred HHHHHHHhcCCCeeeeeecCCCCCCCc
Q 033968 25 NAVRFTLNQDPRVTFCGYSIPHPSDAR 51 (107)
Q Consensus 25 NlLr~~L~~~~~V~fAgY~vpHPle~~ 51 (107)
|-|-..+.+|| |.|+--|-||.+.
T Consensus 28 ~~Li~~i~rdP---fkg~gkpEpLk~~ 51 (84)
T COG4115 28 NELIKEIKRDP---FKGIGKPEPLKGD 51 (84)
T ss_pred HHHHHHhccCc---cccCCCCccCccc
Confidence 44556778887 9999999999765
No 87
>PF09236 AHSP: Alpha-haemoglobin stabilising protein; InterPro: IPR015317 Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle []. ; GO: 0030492 hemoglobin binding, 0006457 protein folding, 0020027 hemoglobin metabolic process, 0030097 hemopoiesis, 0050821 protein stabilization; PDB: 1Y01_A 1XZY_A 3OVU_A 1W0A_A 3IA3_C 1Z8U_A 1W0B_A 1W09_A.
Probab=23.63 E-value=2.1e+02 Score=19.41 Aligned_cols=31 Identities=19% Similarity=0.161 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033968 65 EVLKDSCQELMLMCRHVRSTFAKAVDDFRTS 95 (107)
Q Consensus 65 eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~ 95 (107)
.--.+|++.|...+..+.+.|-...+.|=.+
T Consensus 57 qeqdrAlqel~qeL~tla~pFL~Kyr~fLkS 87 (89)
T PF09236_consen 57 QEQDRALQELQQELNTLANPFLAKYRAFLKS 87 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4457889999999999999998888877543
No 88
>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=23.36 E-value=1.3e+02 Score=19.56 Aligned_cols=23 Identities=22% Similarity=0.343 Sum_probs=13.5
Q ss_pred eeEEEEeCCC--CHH-HHHHHHHHHH
Q 033968 52 VNIRVQTTGD--PAR-EVLKDSCQEL 74 (107)
Q Consensus 52 i~lrIqT~~~--~p~-eal~~Al~~L 74 (107)
..+.|..+.+ ||. +++++|+.+|
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 4456666666 666 7777777654
No 89
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=23.29 E-value=3.3e+02 Score=21.63 Aligned_cols=66 Identities=15% Similarity=0.147 Sum_probs=36.3
Q ss_pred eEEEEecCC-cchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHH
Q 033968 12 ATFSLTEED-HTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELMLMCR 79 (107)
Q Consensus 12 ~~~~i~~ED-HTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~~~~~ 79 (107)
-++.+.|-. =.|.-.|+......|+|.++.|--....... .|.|+.... -.+.+..+++.+...+.
T Consensus 181 ~~~~~~gi~ES~la~~L~~i~~~~~~~~i~s~p~~~~~~~~-~~~i~~~~~-~~~~~~~~~~~~~~~i~ 247 (255)
T COG1058 181 RVLRVFGIGESSLAPTLKDLQDEQPNVTIASYPKDGEVRLR-ELVIRAEAR-DEEEADALLRWLEGRLR 247 (255)
T ss_pred EEEEEcCCChHHHHHHHHHHHhcCCCCEEEecCCCCceecc-ceEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 344444333 3577788888888899998876444333221 344666443 22444444444444433
No 90
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=23.26 E-value=1.2e+02 Score=15.24 Aligned_cols=48 Identities=17% Similarity=0.133 Sum_probs=28.8
Q ss_pred EEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC
Q 033968 13 TFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD 61 (107)
Q Consensus 13 ~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~ 61 (107)
.+...++.-.+..++...-...-.+....+..+++ .+...+.+.+...
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~ 49 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGD-GGEADIFIVVDGD 49 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcCC-CCeEEEEEEEech
Confidence 34555555556666666555566777777666665 4455566665543
No 91
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=23.25 E-value=1.6e+02 Score=22.75 Aligned_cols=38 Identities=16% Similarity=0.281 Sum_probs=27.7
Q ss_pred eeeeecCCCCCCCceeEEEEeCCCCHHHHHHHHHHHHH
Q 033968 38 TFCGYSIPHPSDARVNIRVQTTGDPAREVLKDSCQELM 75 (107)
Q Consensus 38 ~fAgY~vpHPle~~i~lrIqT~~~~p~eal~~Al~~L~ 75 (107)
.|-|...|.---..+.|++.|...++.+.++..++-|.
T Consensus 153 ~fTGid~pYE~P~~Pel~l~t~~~~vee~v~~i~~~l~ 190 (197)
T COG0529 153 NFTGIDSPYEAPENPELHLDTDRNSVEECVEQILDLLK 190 (197)
T ss_pred CCcCCCCCCCCCCCCeeEeccccCCHHHHHHHHHHHHH
Confidence 36677766555567889999988788888777766654
No 92
>PHA02766 hypothetical protein; Provisional
Probab=23.09 E-value=73 Score=20.37 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=30.5
Q ss_pred eeEEEEecCCcchHHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHH
Q 033968 11 NATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQ 72 (107)
Q Consensus 11 ~~~~~i~~EDHTLgNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~ 72 (107)
.+.|+|..||.--. +. .|--..-.||.+++.++|.|+.- +-.+||.--++
T Consensus 16 kisfeineedyqql--ie----------lafsqfiyplndnieikintkeladnekallyeiq 66 (73)
T PHA02766 16 KISFEINEEDYQQL--IE----------LAFSQFIYPLNDNIEIKINTKELADNEKALLYEIQ 66 (73)
T ss_pred EEEEEECHHHHHHH--HH----------HHHHhheeeCCCceEEEechHhhccchhhHhHhhh
Confidence 46778888875321 11 11112346999999999999765 55555544433
No 93
>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=22.72 E-value=2.7e+02 Score=19.33 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=22.4
Q ss_pred CHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhh
Q 033968 62 PAREVLKDSCQELMLM-CRHVRSTFAKAVDDFRTS 95 (107)
Q Consensus 62 ~p~eal~~Al~~L~~~-~~~l~~~f~~a~~~~~~~ 95 (107)
+|.+.|.+..+.|... ++.+..++++++.+|...
T Consensus 98 d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 98 DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 5666666666666543 666777777777777654
No 94
>PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=22.61 E-value=1.3e+02 Score=23.87 Aligned_cols=41 Identities=15% Similarity=0.153 Sum_probs=21.8
Q ss_pred eeeecCCC-CCCCceeEEEEeCCCCHHHHHHHHHHHHHHHHHH
Q 033968 39 FCGYSIPH-PSDARVNIRVQTTGDPAREVLKDSCQELMLMCRH 80 (107)
Q Consensus 39 fAgY~vpH-Ple~~i~lrIqT~~~~p~eal~~Al~~L~~~~~~ 80 (107)
.+||-+|| |+...-.-+ +...+.+.+.+.+|++.+.+.+..
T Consensus 5 v~~~~~sH~P~vg~~~~~-~~~~~~~~~~v~~a~~~~~~~v~~ 46 (278)
T PRK13364 5 IGGITTSHVPAIGGAIAK-GLQQDPYWKPFFDGFPPVREWLEK 46 (278)
T ss_pred hceeecCCCCcccccccc-ccccChhHHHHHHHHHHHHHHHHH
Confidence 46899999 766533222 111113345566666665555543
No 95
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=22.54 E-value=43 Score=24.28 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=16.4
Q ss_pred cCCCeeeeeecCCCCCCCceeEEE
Q 033968 33 QDPRVTFCGYSIPHPSDARVNIRV 56 (107)
Q Consensus 33 ~~~~V~fAgY~vpHPle~~i~lrI 56 (107)
+.....||||+|. |..+.+.+|.
T Consensus 3 ~~e~CsFcG~kIy-PG~G~~fVR~ 25 (131)
T PRK14891 3 ETRTCDYTGEEIE-PGTGTMFVRK 25 (131)
T ss_pred ceeeecCcCCccc-CCCCcEEEec
Confidence 3445789999986 7777766553
No 96
>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=22.10 E-value=1.5e+02 Score=16.15 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 65 EVLKDSCQELMLMCRHVRSTFAKAVDDF 92 (107)
Q Consensus 65 eal~~Al~~L~~~~~~l~~~f~~a~~~~ 92 (107)
..|..++..++..+......|..=-..|
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 3567777777777777777776654444
No 97
>PF13289 SIR2_2: SIR2-like domain
Probab=21.82 E-value=95 Score=20.55 Aligned_cols=26 Identities=31% Similarity=0.487 Sum_probs=18.9
Q ss_pred cchHHHHHHHHhcCCCeeeeeecCCCC
Q 033968 21 HTLANAVRFTLNQDPRVTFCGYSIPHP 47 (107)
Q Consensus 21 HTLgNlLr~~L~~~~~V~fAgY~vpHP 47 (107)
-.+.+.|+..+ +...+.|.||...-|
T Consensus 74 ~~~~~~l~~~l-~~~~~lfiGys~~D~ 99 (143)
T PF13289_consen 74 PWFPNFLRSLL-RSKTLLFIGYSFNDP 99 (143)
T ss_pred HHHHHHHHHHH-cCCCEEEEEECCCCH
Confidence 34566777666 677899999997655
No 98
>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=21.56 E-value=1.8e+02 Score=16.75 Aligned_cols=45 Identities=18% Similarity=0.210 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHH
Q 033968 24 ANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQE 73 (107)
Q Consensus 24 gNlLr~~L~~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~ 73 (107)
-+.++..|.+.|+|.-+-...+ .+. +.|..+.. ...+.+.++++.
T Consensus 13 ~~~v~~~l~~~~GV~~v~vd~~---~~~--v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 13 AKKVEKALSKLPGVKSVKVDLE---TKT--VTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp HHHHHHHHHTSTTEEEEEEETT---TTE--EEEEESTTTSCHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCcEEEEECC---CCE--EEEEEecCCCCHHHHHHHHHH
Confidence 4678889999999977666554 344 44555444 334777777765
No 99
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=21.39 E-value=2.6e+02 Score=25.01 Aligned_cols=44 Identities=14% Similarity=0.080 Sum_probs=33.4
Q ss_pred eeEEEEeCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033968 52 VNIRVQTTGD-PAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTS 95 (107)
Q Consensus 52 i~lrIqT~~~-~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~ 95 (107)
.+..++-++= +.+-||++++..|+.+...++..++++.+..+.-
T Consensus 605 ~~~vleekslvdtvyalkd~v~~lqqd~~kmkk~leeEqkaRrdL 649 (661)
T KOG2070|consen 605 GQSVLEEKSLVDTVYALKDEVSELQQDNKKMKKVLEEEQKARRDL 649 (661)
T ss_pred cceeecccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444443443 7788999999999999999999999887765543
No 100
>PF10203 Pet191_N: Cytochrome c oxidase assembly protein PET191; InterPro: IPR018793 This entry represents a family of conserved proteins found from nematodes to humans. Cytochrome c oxidase assembly protein Pet191 carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex [].
Probab=21.21 E-value=49 Score=21.07 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033968 59 TGDPAREVLKDSCQELMLMCRHVRSTFAKA 88 (107)
Q Consensus 59 ~~~~p~eal~~Al~~L~~~~~~l~~~f~~a 88 (107)
.+.+|.+.|++...++-..|..++..|-+-
T Consensus 25 ~~~t~~~Cl~~~~~~~p~eC~~lr~~f~eC 54 (68)
T PF10203_consen 25 EKRTPKDCLKDPSDELPEECQQLRKAFFEC 54 (68)
T ss_pred CCCCHHHHHcCCCCcCCHHHHHHHHHHHHH
Confidence 344999999999999999999999998763
No 101
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=20.99 E-value=2.9e+02 Score=19.53 Aligned_cols=29 Identities=21% Similarity=0.375 Sum_probs=20.1
Q ss_pred cCCCeeeeeecCCCCCCCceeE----EEEeCCC
Q 033968 33 QDPRVTFCGYSIPHPSDARVNI----RVQTTGD 61 (107)
Q Consensus 33 ~~~~V~fAgY~vpHPle~~i~l----rIqT~~~ 61 (107)
=||+..-+||-+-=...+++.+ .|+|+.+
T Consensus 5 IDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~ 37 (154)
T cd00529 5 IDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSD 37 (154)
T ss_pred EccCcCceEEEEEEeeCCeEEEEEeeEEECCCC
Confidence 3888889999986443455555 6788755
No 102
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=20.61 E-value=1.9e+02 Score=22.49 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=22.9
Q ss_pred eeEEEEeCCC---CHHHHHHHHHHHHHHHHH
Q 033968 52 VNIRVQTTGD---PAREVLKDSCQELMLMCR 79 (107)
Q Consensus 52 i~lrIqT~~~---~p~eal~~Al~~L~~~~~ 79 (107)
+.|-+.|+|. .|+++|..++..+++.+.
T Consensus 6 ~~lllDtSgSM~Ge~IealN~Glq~m~~~Lk 36 (207)
T COG4245 6 CYLLLDTSGSMIGEPIEALNAGLQMMIDTLK 36 (207)
T ss_pred EEEEEecCcccccccHHHHHHHHHHHHHHHH
Confidence 5677888876 899999999988877664
No 103
>cd07931 eukaryotic_phosphagen_kinases Phosphagen (guanidino) kinases mostly found in eukaryotes. 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 k
Probab=20.44 E-value=4.3e+02 Score=21.79 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=13.3
Q ss_pred EEEEe--CCCCHHHHHHHHHHHH
Q 033968 54 IRVQT--TGDPAREVLKDSCQEL 74 (107)
Q Consensus 54 lrIqT--~~~~p~eal~~Al~~L 74 (107)
|||+. .|++..+|+.+++.-+
T Consensus 209 lRIism~~G~~l~~vf~r~~~~~ 231 (338)
T cd07931 209 LRIISMQKGGDLKAVFTRLSRAL 231 (338)
T ss_pred EEEEEecCCCCHHHHHHHHHHHH
Confidence 66766 4448777777666443
No 104
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=20.39 E-value=4.2e+02 Score=20.81 Aligned_cols=45 Identities=20% Similarity=0.244 Sum_probs=29.7
Q ss_pred cCCCeeeeeecCCCCCCCceeEEEEeCCC-CHHHHHHHHHHHHHHHHHH
Q 033968 33 QDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDSCQELMLMCRH 80 (107)
Q Consensus 33 ~~~~V~fAgY~vpHPle~~i~lrIqT~~~-~p~eal~~Al~~L~~~~~~ 80 (107)
..++|..-=|.|-=| .-.|++++.+- ...++|++|++.+.+.+..
T Consensus 205 ~~~~~~v~i~~ig~P---~Y~i~~~~~d~k~~~~~l~~~~~~~~~~i~~ 250 (262)
T PRK03987 205 KYEDVEVEIYYVGAP---RYRIDVTAPDYKTAEKALKKIAERAIKVIKK 250 (262)
T ss_pred CCCCCcEEEEEECCC---eEEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555544555544 45666776655 7888899888888776654
No 105
>PF07083 DUF1351: Protein of unknown function (DUF1351); InterPro: IPR009785 This entry is represented by Lactobacillus prophage Lj928, Orf309. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown.
Probab=20.28 E-value=3.4e+02 Score=20.56 Aligned_cols=37 Identities=14% Similarity=0.239 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 033968 62 PAREVLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKV 98 (107)
Q Consensus 62 ~p~eal~~Al~~L~~~~~~l~~~f~~a~~~~~~~~~~ 98 (107)
.|.+.++.-+..|...++...+.++..++.|......
T Consensus 71 ~P~~~Fe~~~K~l~~~i~~~~~~I~~~ik~~Ee~~k~ 107 (215)
T PF07083_consen 71 KPIKEFEAKIKELIAPIDEASDKIDEQIKEFEEKEKE 107 (215)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6888888888899999999999998888888776653
No 106
>KOG0762 consensus Mitochondrial carrier protein [Energy production and conversion]
Probab=20.18 E-value=84 Score=25.58 Aligned_cols=23 Identities=35% Similarity=0.609 Sum_probs=19.1
Q ss_pred eeecCCCCCCCceeEEEEeCCC-CH
Q 033968 40 CGYSIPHPSDARVNIRVQTTGD-PA 63 (107)
Q Consensus 40 AgY~vpHPle~~i~lrIqT~~~-~p 63 (107)
||--+-||++ .+.+|.||.+. +|
T Consensus 25 AGVl~GhPlD-TvkVrlQtqs~~~P 48 (311)
T KOG0762|consen 25 AGVLVGHPLD-TVKVRLQTQSSKSP 48 (311)
T ss_pred ceeeecCCcc-eeEEEEeccCCCCC
Confidence 7788999986 78999999776 65
No 107
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=20.15 E-value=74 Score=23.49 Aligned_cols=16 Identities=13% Similarity=0.345 Sum_probs=13.1
Q ss_pred CCCHHHHHHHHHHHHH
Q 033968 60 GDPAREVLKDSCQELM 75 (107)
Q Consensus 60 ~~~p~eal~~Al~~L~ 75 (107)
|.+|+++|.+|++++.
T Consensus 54 g~~Piqvf~~Ai~N~~ 69 (148)
T COG0049 54 GQNPLQVFEKAIENVK 69 (148)
T ss_pred CCChHHHHHHHHHhcC
Confidence 3489999999998764
No 108
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=20.15 E-value=2e+02 Score=16.87 Aligned_cols=30 Identities=10% Similarity=0.226 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033968 65 EVLKDSCQELMLMCRHVRSTFAKAVDDFRT 94 (107)
Q Consensus 65 eal~~Al~~L~~~~~~l~~~f~~a~~~~~~ 94 (107)
.-+..+..++...+..+.+.+..+...|..
T Consensus 54 ~~~~~~~~~~~~~L~~~~~~l~~~~~~~~~ 83 (86)
T PF06013_consen 54 EEWNQAFRQLNEALEELSQALRQAAQNYEQ 83 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334455555555555555555555555544
Done!