Query 034762
Match_columns 84
No_of_seqs 101 out of 403
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:11:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034762hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4392 RNA polymerase, subuni 100.0 2.6E-38 5.6E-43 214.7 8.2 82 1-82 1-82 (117)
2 cd06926 RNAP_II_RPB11 RPB11 su 100.0 4.1E-32 8.9E-37 177.7 8.7 70 13-82 1-70 (93)
3 PRK01146 DNA-directed RNA poly 100.0 6.2E-29 1.3E-33 160.6 7.8 63 18-82 2-64 (85)
4 cd07029 RNAP_I_III_AC19 AC19 s 100.0 8.6E-29 1.9E-33 159.9 7.1 59 24-82 4-62 (85)
5 cd06927 RNAP_L L subunit of Ar 100.0 1.5E-28 3.2E-33 158.2 7.9 61 20-82 2-62 (83)
6 cd07027 RNAP_RPB11_like RPB11 100.0 2.3E-28 5E-33 157.3 7.8 57 26-82 6-62 (83)
7 PF13656 RNA_pol_L_2: RNA poly 100.0 1.1E-28 2.3E-33 156.6 5.2 54 29-82 1-54 (77)
8 COG1761 RPB11 DNA-directed RNA 99.9 1.1E-25 2.3E-30 149.8 8.4 65 16-80 2-66 (99)
9 KOG3438 DNA-directed RNA polym 99.9 2.1E-25 4.6E-30 149.4 6.0 56 27-82 14-69 (105)
10 cd00460 RNAP_RPB11_RPB3 RPB11 99.9 1.9E-21 4E-26 124.8 7.4 56 26-82 6-67 (86)
11 PF01193 RNA_pol_L: RNA polyme 99.3 1.5E-12 3.2E-17 79.4 3.7 48 31-82 1-49 (66)
12 PRK00783 DNA-directed RNA poly 96.3 0.0054 1.2E-07 45.6 4.0 34 18-53 2-35 (263)
13 cd07030 RNAP_D D subunit of Ar 96.0 0.01 2.2E-07 44.0 4.0 34 18-53 2-35 (259)
14 cd07028 RNAP_RPB3_like RPB3 su 95.5 0.024 5.1E-07 41.8 4.2 40 19-60 3-48 (212)
15 PRK05182 DNA-directed RNA poly 94.7 0.054 1.2E-06 41.9 4.3 46 18-63 8-58 (310)
16 PRK14979 DNA-directed RNA poly 94.6 0.048 1E-06 40.0 3.7 37 20-57 5-42 (195)
17 cd07031 RNAP_II_RPB3 RPB3 subu 94.4 0.059 1.3E-06 40.7 4.0 34 18-53 2-35 (265)
18 cd06928 RNAP_alpha_NTD N-termi 93.9 0.065 1.4E-06 39.3 3.1 38 25-62 5-47 (215)
19 COG0202 RpoA DNA-directed RNA 92.7 0.19 4.2E-06 39.2 4.2 42 19-60 7-51 (317)
20 smart00662 RPOLD RNA polymeras 92.0 0.15 3.3E-06 37.4 2.8 32 31-62 2-34 (224)
21 CHL00013 rpoA RNA polymerase a 89.4 1.2 2.6E-05 34.9 5.8 47 19-65 10-61 (327)
22 COG2805 PilT Tfp pilus assembl 82.3 1.2 2.6E-05 35.7 2.6 23 38-60 183-205 (353)
23 TIGR02027 rpoA DNA-directed RN 82.0 1.3 2.9E-05 34.0 2.7 28 36-63 11-39 (297)
24 cd07032 RNAP_I_II_AC40 AC40 su 75.3 5.3 0.00012 30.9 4.2 34 18-53 2-35 (291)
25 PRK02261 methylaspartate mutas 62.2 8.8 0.00019 26.1 2.7 36 28-63 4-41 (137)
26 TIGR02370 pyl_corrinoid methyl 50.7 18 0.00039 25.8 2.8 37 28-64 85-123 (197)
27 cd02067 B12-binding B12 bindin 47.3 21 0.00045 22.8 2.5 27 31-57 3-29 (119)
28 PF03633 Glyco_hydro_65C: Glyc 46.0 22 0.00048 20.1 2.2 25 17-42 28-52 (54)
29 cd02069 methionine_synthase_B1 43.6 26 0.00056 25.5 2.7 37 28-64 89-127 (213)
30 cd02071 MM_CoA_mut_B12_BD meth 41.3 25 0.00054 22.9 2.2 27 31-57 3-29 (122)
31 cd02070 corrinoid_protein_B12- 40.7 23 0.00049 25.1 2.0 39 28-66 83-123 (201)
32 COG2804 PulE Type II secretory 35.5 35 0.00077 28.6 2.6 24 37-60 311-334 (500)
33 COG5015 Uncharacterized conser 35.0 28 0.00061 24.5 1.7 20 45-64 48-67 (132)
34 KOG0359 Chaperonin complex com 34.9 48 0.001 27.9 3.3 29 15-43 348-377 (520)
35 KOG1522 RNA polymerase II, sub 33.2 71 0.0015 25.0 3.8 38 16-55 5-43 (285)
36 PF00437 T2SE: Type II/IV secr 32.2 1.7E+02 0.0037 21.0 5.5 33 28-60 172-204 (270)
37 PF05986 ADAM_spacer1: ADAM-TS 31.0 1.5E+02 0.0033 19.2 5.3 71 5-77 15-99 (114)
38 TIGR02533 type_II_gspE general 29.0 1.3E+02 0.0028 24.6 4.9 22 39-60 297-318 (486)
39 KOG1521 RNA polymerase I and I 28.5 57 0.0012 26.1 2.6 36 16-53 45-80 (338)
40 COG0634 Hpt Hypoxanthine-guani 27.4 74 0.0016 23.3 2.9 20 35-54 102-121 (178)
41 cd01129 PulE-GspE PulE/GspE Th 25.4 2.6E+02 0.0057 20.7 5.6 29 32-60 127-156 (264)
42 TIGR02782 TrbB_P P-type conjug 25.1 2.8E+02 0.006 21.1 5.8 32 28-60 179-211 (299)
43 PF08478 POTRA_1: POTRA domain 23.9 1.2E+02 0.0027 17.1 3.0 31 44-76 37-67 (69)
44 PF08712 Nfu_N: Scaffold prote 22.8 2E+02 0.0043 18.1 4.0 36 27-62 20-55 (87)
45 PHA02781 hypothetical protein; 22.3 88 0.0019 19.8 2.2 27 17-43 6-32 (78)
46 PF04263 TPK_catalytic: Thiami 22.2 52 0.0011 22.0 1.2 15 38-52 98-112 (123)
47 TIGR02538 type_IV_pilB type IV 21.5 2.6E+02 0.0057 23.2 5.4 28 33-60 364-392 (564)
48 PF01933 UPF0052: Uncharacteri 21.1 62 0.0013 25.0 1.6 15 37-51 84-98 (300)
49 PRK10436 hypothetical protein; 21.0 1.5E+02 0.0033 24.2 3.9 22 39-60 273-294 (462)
No 1
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=100.00 E-value=2.6e-38 Score=214.66 Aligned_cols=82 Identities=54% Similarity=0.904 Sum_probs=80.3
Q ss_pred CCCCcccceeeeCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762 1 MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH 80 (84)
Q Consensus 1 mn~p~~~~~~~l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~ 80 (84)
||||+|||+|+|++|++||++..++|.+|++.|+|.+|||||||+|+.+|++||+|.||||++|||+.+++.|||||+.+
T Consensus 1 MNaP~~fE~fll~eg~kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqtt~d 80 (117)
T KOG4392|consen 1 MNAPPAFESFLLFEGEKKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQTTED 80 (117)
T ss_pred CCCchhhhhheeccCCceeEEecCCCCCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred cc
Q 034762 81 SR 82 (84)
Q Consensus 81 ~~ 82 (84)
.+
T Consensus 81 ~~ 82 (117)
T KOG4392|consen 81 CS 82 (117)
T ss_pred CC
Confidence 54
No 2
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=99.97 E-value=4.1e-32 Score=177.70 Aligned_cols=70 Identities=57% Similarity=0.929 Sum_probs=67.8
Q ss_pred CCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 13 PEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 13 ~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
|+|++||++..+++++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+
T Consensus 1 ~~~~~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~ 70 (93)
T cd06926 1 PEGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSIT 70 (93)
T ss_pred CCCccceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCC
Confidence 6899999999999999999999999999999999999999999999999999999999999999998654
No 3
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=99.96 E-value=6.2e-29 Score=160.55 Aligned_cols=63 Identities=27% Similarity=0.363 Sum_probs=57.7
Q ss_pred eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
++++.. +.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+
T Consensus 2 ~ikvi~--~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~ 64 (85)
T PRK01146 2 EIKVLE--KEDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGID 64 (85)
T ss_pred eEEEEe--cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCC
Confidence 345554 679999999999999999999999999999999999999999999999999997754
No 4
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=99.95 E-value=8.6e-29 Score=159.89 Aligned_cols=59 Identities=32% Similarity=0.546 Sum_probs=56.0
Q ss_pred cCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 24 DTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 24 ~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
..+.+|+++|+|.||||||||+||++|+++|+|+||||+||||+++++.|||||+++.+
T Consensus 4 ~~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~ 62 (85)
T cd07029 4 EGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEP 62 (85)
T ss_pred ccCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCC
Confidence 45789999999999999999999999999999999999999999999999999998654
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=99.95 E-value=1.5e-28 Score=158.22 Aligned_cols=61 Identities=30% Similarity=0.395 Sum_probs=56.3
Q ss_pred EEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 20 SYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 20 ~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
++.+ +.+|+++|+|.||||||||+||++|+++|+|.||||+|||||+++++|||||+++.+
T Consensus 2 kvi~--~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~ 62 (83)
T cd06927 2 KVIE--KEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVD 62 (83)
T ss_pred eEEE--cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCC
Confidence 3444 569999999999999999999999999999999999999999999999999999654
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=99.95 E-value=2.3e-28 Score=157.31 Aligned_cols=57 Identities=37% Similarity=0.595 Sum_probs=54.2
Q ss_pred CCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 26 ~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
+.+|+++|+|.||||||||+||++|+++|+|+||||+||||++++++|||||+++.+
T Consensus 6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrI~T~~~~~ 62 (83)
T cd07027 6 KEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIK 62 (83)
T ss_pred cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCCCCCccEEEEEECCCCC
Confidence 558999999999999999999999999999999999999999999999999998653
No 7
>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=99.95 E-value=1.1e-28 Score=156.56 Aligned_cols=54 Identities=46% Similarity=0.781 Sum_probs=49.5
Q ss_pred ceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 29 n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
|+++|+|.+|||||||+||++|+++|+|+||||+|||||+++++|||||+++.+
T Consensus 1 n~~~f~i~~EDHTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~ 54 (77)
T PF13656_consen 1 NEITFTIYGEDHTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGIT 54 (77)
T ss_dssp TEEEEEEES--HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-
T ss_pred CeEEEEEeCCCccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCC
Confidence 689999999999999999999999999999999999999999999999998843
No 8
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=99.93 E-value=1.1e-25 Score=149.78 Aligned_cols=65 Identities=37% Similarity=0.532 Sum_probs=60.7
Q ss_pred ceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccC
Q 034762 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKH 80 (84)
Q Consensus 16 e~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~ 80 (84)
.+++++...++.+|+++|++.||||||||+|+++|+++++|+||+|+||||+.+++.+||||+++
T Consensus 2 ~~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~ 66 (99)
T COG1761 2 TPEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGG 66 (99)
T ss_pred CCceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCC
Confidence 45666666668899999999999999999999999999999999999999999999999999998
No 9
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=99.92 E-value=2.1e-25 Score=149.36 Aligned_cols=56 Identities=34% Similarity=0.654 Sum_probs=53.2
Q ss_pred CcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 27 ~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
..++.+|++..|||||||+||++|+++|+|+||||.||||+++++.|||||.++..
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~ 69 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDP 69 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCc
Confidence 67899999999999999999999999999999999999999999999999997653
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=99.85 E-value=1.9e-21 Score=124.78 Aligned_cols=56 Identities=39% Similarity=0.559 Sum_probs=53.3
Q ss_pred CCcceeEEEEecCCcchHHHHHHHHhcCCceeEEeeeCCCCC------CcceEEEEEeccCcc
Q 034762 26 KIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPL------QYKIIVRAELAKHSR 82 (84)
Q Consensus 26 ~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~vpHPl------~~~i~l~Iqt~~~~~ 82 (84)
+.+|+++|+|.||||||||+||++|++ +.|.||||+|+||+ .++++|+|+|+|+.+
T Consensus 6 ~~~~~~~~~~~~edhTl~n~L~~~l~~-~pV~~a~Y~v~hp~~~~~~~~d~~~~~VeT~Gs~~ 67 (86)
T cd00460 6 KEKNYVDFVLENEDHTLGNSLRRILLK-SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIP 67 (86)
T ss_pred CCCCEEEEEEeCCCchHHHHHHHHHhC-CCceEEEEEeCCCccCCCCCCCeEEEEEEECCCCC
Confidence 568999999999999999999999999 99999999999999 999999999999754
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=99.32 E-value=1.5e-12 Score=79.41 Aligned_cols=48 Identities=33% Similarity=0.512 Sum_probs=45.0
Q ss_pred eEEEEecCCcchHHHHHHHHhcC-CceeEEeeeCCCCCCcceEEEEEeccCcc
Q 034762 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYKLPHPLQYKIIVRAELAKHSR 82 (84)
Q Consensus 31 ~~~~i~~EdHTLgNlLr~~Ll~~-~~V~fAgY~vpHPl~~~i~l~Iqt~~~~~ 82 (84)
++|.+.|+|||+||+||..|+++ |.|.+++ ||..++++|+|+|+|+.+
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~ 49 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLT 49 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCC
Confidence 57999999999999999999999 9999999 999999999999999854
No 12
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=96.32 E-value=0.0054 Score=45.60 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=29.4
Q ss_pred eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (84)
Q Consensus 18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~ 53 (84)
||++.+.+ ++.++|.+.|-++||||+||..|+..
T Consensus 2 ~~~~~~~~--~~~~~f~~~g~~~t~~NalRRvlls~ 35 (263)
T PRK00783 2 EIEILELD--DRSARFVVEGVTPAFANAIRRAMIAD 35 (263)
T ss_pred ceEEEEcC--CcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence 56776654 68899999999999999999999975
No 13
>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=95.98 E-value=0.01 Score=44.04 Aligned_cols=34 Identities=15% Similarity=0.195 Sum_probs=29.4
Q ss_pred eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (84)
Q Consensus 18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~ 53 (84)
+|++.+.+ ++.++|.+.|-|+|+||+||..|+..
T Consensus 2 ~~~~~~~~--~~~~~f~~~g~~~s~~NalRRills~ 35 (259)
T cd07030 2 EIEVLELD--DDRARFVLEGVPPAFANAIRRAIISE 35 (259)
T ss_pred ceEEEecC--CCEEEEEEeCCCHHHHHHHHHHHHhc
Confidence 56776644 68999999999999999999999875
No 14
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=95.49 E-value=0.024 Score=41.81 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=32.0
Q ss_pred eEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC-C-----ceeEEe
Q 034762 19 VSYERDTKIINAASFTIEREEHTIGNILRMQLHRD-E-----NVLFAG 60 (84)
Q Consensus 19 i~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~-~-----~V~fAg 60 (84)
|++.+ +.++.++|.+.|-|+|+||+||..|+.. | .|.+.+
T Consensus 3 i~i~~--~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~ 48 (212)
T cd07028 3 VKIRE--ADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVET 48 (212)
T ss_pred EEEEE--cCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEc
Confidence 45555 5589999999999999999999999985 3 555555
No 15
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=94.68 E-value=0.054 Score=41.93 Aligned_cols=46 Identities=26% Similarity=0.323 Sum_probs=33.3
Q ss_pred eeEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-CceeEEeeeC
Q 034762 18 KVSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKL 63 (84)
Q Consensus 18 Ki~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V~fAgY~v 63 (84)
++++...+..++.++|.+. |.++|+||+||..|+.. |+.-.-+-+|
T Consensus 8 ~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI 58 (310)
T PRK05182 8 KIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKI 58 (310)
T ss_pred EEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEE
Confidence 4555543335789999997 99999999999999884 5544444433
No 16
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=94.61 E-value=0.048 Score=40.01 Aligned_cols=37 Identities=14% Similarity=0.197 Sum_probs=29.9
Q ss_pred EEeecCCCcceeEEEEecCCcchHHHHHHHHhcC-Ccee
Q 034762 20 SYERDTKIINAASFTIEREEHTIGNILRMQLHRD-ENVL 57 (84)
Q Consensus 20 ~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~-~~V~ 57 (84)
++...++..+.++|.+. -+.|+||+||..|+.. |..-
T Consensus 5 ~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~A 42 (195)
T PRK14979 5 KEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYA 42 (195)
T ss_pred ceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCccee
Confidence 34445578999999999 9999999999999874 5433
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=94.44 E-value=0.059 Score=40.75 Aligned_cols=34 Identities=21% Similarity=0.312 Sum_probs=28.9
Q ss_pred eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (84)
Q Consensus 18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~ 53 (84)
+|++.+.+ ++.++|.+.+=|+|+||+||..|+..
T Consensus 2 ~i~i~~~~--~~~~~F~l~~~~~s~aNALRRillse 35 (265)
T cd07031 2 RVEITELT--DDKVKFILENTDLSVANSLRRVMIAE 35 (265)
T ss_pred cEEEEEcC--CCEEEEEEEcCcHHHHHHHHHHHHHc
Confidence 46666644 78999999999999999999999874
No 18
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=93.86 E-value=0.065 Score=39.29 Aligned_cols=38 Identities=29% Similarity=0.329 Sum_probs=29.1
Q ss_pred CCCcceeEEEE----ecCCcchHHHHHHHHhcC-CceeEEeee
Q 034762 25 TKIINAASFTI----EREEHTIGNILRMQLHRD-ENVLFAGYK 62 (84)
Q Consensus 25 ~~~~n~~~~~i----~~EdHTLgNlLr~~Ll~~-~~V~fAgY~ 62 (84)
+...++++|.| .|.++|+||+||..|+.. |+.-+-+-+
T Consensus 5 ~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~ 47 (215)
T cd06928 5 NKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVK 47 (215)
T ss_pred cCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEE
Confidence 34478899999 779999999999999885 554444433
No 19
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=92.67 E-value=0.19 Score=39.16 Aligned_cols=42 Identities=19% Similarity=-0.005 Sum_probs=31.2
Q ss_pred eEEeecC--CCcceeEEEEecCCcchHHHHHHHHhc-CCceeEEe
Q 034762 19 VSYERDT--KIINAASFTIEREEHTIGNILRMQLHR-DENVLFAG 60 (84)
Q Consensus 19 i~~~~~~--~~~n~~~~~i~~EdHTLgNlLr~~Ll~-~~~V~fAg 60 (84)
|++...+ ..+-.+++.+.|-+|||||+||..|+. .|..-.-+
T Consensus 7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~ 51 (317)
T COG0202 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTA 51 (317)
T ss_pred eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEE
Confidence 5555443 347789999999999999999999987 46544333
No 20
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=92.04 E-value=0.15 Score=37.40 Aligned_cols=32 Identities=25% Similarity=0.279 Sum_probs=25.2
Q ss_pred eEEEEecCCcchHHHHHHHHhcC-CceeEEeee
Q 034762 31 ASFTIEREEHTIGNILRMQLHRD-ENVLFAGYK 62 (84)
Q Consensus 31 ~~~~i~~EdHTLgNlLr~~Ll~~-~~V~fAgY~ 62 (84)
++|.+.+-++|+||+||..|+.. |..-.-+.+
T Consensus 2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~ 34 (224)
T smart00662 2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVE 34 (224)
T ss_pred eEEEEEcCCchHHHHHHHHHHHcCccceEEEEE
Confidence 67999999999999999999884 554444433
No 21
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=89.40 E-value=1.2 Score=34.95 Aligned_cols=47 Identities=26% Similarity=0.301 Sum_probs=34.6
Q ss_pred eEEeecCCCcceeEEEEe----cCCcchHHHHHHHHhcC-CceeEEeeeCCC
Q 034762 19 VSYERDTKIINAASFTIE----REEHTIGNILRMQLHRD-ENVLFAGYKLPH 65 (84)
Q Consensus 19 i~~~~~~~~~n~~~~~i~----~EdHTLgNlLr~~Ll~~-~~V~fAgY~vpH 65 (84)
++........++.+|.|. |..|||||+||..|+.. |+.-+.+-++.+
T Consensus 10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 455555667888999986 56679999999999984 666666655533
No 22
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=82.31 E-value=1.2 Score=35.66 Aligned_cols=23 Identities=30% Similarity=0.592 Sum_probs=21.3
Q ss_pred CCcchHHHHHHHHhcCCceeEEe
Q 034762 38 EEHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 38 EdHTLgNlLr~~Ll~~~~V~fAg 60 (84)
-+|++.|.||..|.+||+|.+.|
T Consensus 183 dT~sF~~aLraALReDPDVIlvG 205 (353)
T COG2805 183 DTLSFANALRAALREDPDVILVG 205 (353)
T ss_pred cHHHHHHHHHHHhhcCCCEEEEe
Confidence 45999999999999999999988
No 23
>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=82.04 E-value=1.3 Score=33.99 Aligned_cols=28 Identities=25% Similarity=0.253 Sum_probs=21.1
Q ss_pred ecCCcchHHHHHHHHhcC-CceeEEeeeC
Q 034762 36 EREEHTIGNILRMQLHRD-ENVLFAGYKL 63 (84)
Q Consensus 36 ~~EdHTLgNlLr~~Ll~~-~~V~fAgY~v 63 (84)
.|-++||||+||..|+.. |++-..+-+|
T Consensus 11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI 39 (297)
T TIGR02027 11 RGFGITLGNALRRVLLSSIPGAAITAVKI 39 (297)
T ss_pred CCchhHHHHHHHHHHHhcCCceEEEEEEE
Confidence 477899999999999985 6655555443
No 24
>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=75.25 E-value=5.3 Score=30.95 Aligned_cols=34 Identities=18% Similarity=0.155 Sum_probs=29.0
Q ss_pred eeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762 18 KVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (84)
Q Consensus 18 Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~ 53 (84)
||++.+. .++.++|.+.|-|=.+.|+||..|+..
T Consensus 2 ~i~i~~~--~~~~~~f~l~~~d~s~ANAlRRimiaE 35 (291)
T cd07032 2 KIEIISL--SDEELEFDLIGVDASIANAFRRILLAE 35 (291)
T ss_pred eEEEEEC--CCCEEEEEEecCCHHHHHHHHHHHHhc
Confidence 5667664 479999999999999999999998864
No 25
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=62.17 E-value=8.8 Score=26.12 Aligned_cols=36 Identities=17% Similarity=0.143 Sum_probs=27.2
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCc--eeEEeeeC
Q 034762 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKL 63 (84)
Q Consensus 28 ~n~~~~~i~~EdHTLgNlLr~~Ll~~~~--V~fAgY~v 63 (84)
+.-+..++.+|.|.+|..+-..+++..+ |.+-|-++
T Consensus 4 ~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~v 41 (137)
T PRK02261 4 KTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMT 41 (137)
T ss_pred CEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCC
Confidence 3456788999999999999999999875 44444444
No 26
>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=50.69 E-value=18 Score=25.76 Aligned_cols=37 Identities=22% Similarity=0.297 Sum_probs=29.2
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCc--eeEEeeeCC
Q 034762 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLP 64 (84)
Q Consensus 28 ~n~~~~~i~~EdHTLgNlLr~~Ll~~~~--V~fAgY~vp 64 (84)
..-+..++.||.|.||..+...+++..+ |.+.|-++|
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp 123 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVP 123 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCC
Confidence 4557789999999999999999999874 555555554
No 27
>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=47.29 E-value=21 Score=22.75 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=22.2
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCcee
Q 034762 31 ASFTIEREEHTIGNILRMQLHRDENVL 57 (84)
Q Consensus 31 ~~~~i~~EdHTLgNlLr~~Ll~~~~V~ 57 (84)
+-....+|.|++|..+-..+++..+.+
T Consensus 3 l~~~~~~e~H~lG~~~~~~~l~~~G~~ 29 (119)
T cd02067 3 VIATVGGDGHDIGKNIVARALRDAGFE 29 (119)
T ss_pred EEEeeCCchhhHHHHHHHHHHHHCCCE
Confidence 456788999999999999999877544
No 28
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=46.03 E-value=22 Score=20.07 Aligned_cols=25 Identities=20% Similarity=0.133 Sum_probs=11.9
Q ss_pred eeeEEeecCCCcceeEEEEecCCcch
Q 034762 17 KKVSYERDTKIINAASFTIEREEHTI 42 (84)
Q Consensus 17 ~Ki~~~~~~~~~n~~~~~i~~EdHTL 42 (84)
.++++...+.. ..+++.+.|+.++|
T Consensus 28 ~~v~v~~~~g~-~~l~i~v~g~~~~L 52 (54)
T PF03633_consen 28 EKVTVTLLSGD-APLTIKVYGEEVTL 52 (54)
T ss_dssp TEEEEEEEESS---EEEEETT-----
T ss_pred CEEEEEEccCC-ccEEEEECCCcccc
Confidence 44555554444 57889999999886
No 29
>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=43.55 E-value=26 Score=25.50 Aligned_cols=37 Identities=22% Similarity=0.250 Sum_probs=28.6
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCc--eeEEeeeCC
Q 034762 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLP 64 (84)
Q Consensus 28 ~n~~~~~i~~EdHTLgNlLr~~Ll~~~~--V~fAgY~vp 64 (84)
..-+..++.||.|.||-.+...+++..+ |.+-|-++|
T Consensus 89 ~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp 127 (213)
T cd02069 89 GKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVP 127 (213)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCC
Confidence 4557788999999999999999999874 455554444
No 30
>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=41.33 E-value=25 Score=22.91 Aligned_cols=27 Identities=15% Similarity=0.051 Sum_probs=23.0
Q ss_pred eEEEEecCCcchHHHHHHHHhcCCcee
Q 034762 31 ASFTIEREEHTIGNILRMQLHRDENVL 57 (84)
Q Consensus 31 ~~~~i~~EdHTLgNlLr~~Ll~~~~V~ 57 (84)
+..++.+|.|.+|..+-..+++..+.+
T Consensus 3 v~~~~~gd~H~lG~~~~~~~l~~~G~~ 29 (122)
T cd02071 3 LVAKPGLDGHDRGAKVIARALRDAGFE 29 (122)
T ss_pred EEEecCCChhHHHHHHHHHHHHHCCCE
Confidence 557889999999999999999987554
No 31
>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=40.68 E-value=23 Score=25.13 Aligned_cols=39 Identities=23% Similarity=0.254 Sum_probs=29.0
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCc--eeEEeeeCCCC
Q 034762 28 INAASFTIEREEHTIGNILRMQLHRDEN--VLFAGYKLPHP 66 (84)
Q Consensus 28 ~n~~~~~i~~EdHTLgNlLr~~Ll~~~~--V~fAgY~vpHP 66 (84)
..-+..++.||.|+||-.+...+++..+ |.+.|-.+|..
T Consensus 83 ~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~ 123 (201)
T cd02070 83 GKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPE 123 (201)
T ss_pred CeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHH
Confidence 3456788999999999999999998875 44556555543
No 32
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=35.54 E-value=35 Score=28.60 Aligned_cols=24 Identities=29% Similarity=0.472 Sum_probs=21.7
Q ss_pred cCCcchHHHHHHHHhcCCceeEEe
Q 034762 37 REEHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 37 ~EdHTLgNlLr~~Ll~~~~V~fAg 60 (84)
.-+=|+.++||..|.+||+|.+.|
T Consensus 311 k~gltfa~~LRa~LRqDPDvImVG 334 (500)
T COG2804 311 KIGLTFARALRAILRQDPDVIMVG 334 (500)
T ss_pred ccCCCHHHHHHHHhccCCCeEEEe
Confidence 346899999999999999999987
No 33
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=35.03 E-value=28 Score=24.46 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=16.6
Q ss_pred HHHHHHhcCCceeEEeeeCC
Q 034762 45 ILRMQLHRDENVLFAGYKLP 64 (84)
Q Consensus 45 lLr~~Ll~~~~V~fAgY~vp 64 (84)
.+=.+|.++|+|+|||-.-.
T Consensus 48 ~~yKqik~np~vefcg~~kd 67 (132)
T COG5015 48 PYYKQIKKNPEVEFCGMDKD 67 (132)
T ss_pred HHHHHHhhCCCeEEEEecCC
Confidence 46689999999999997643
No 34
>KOG0359 consensus Chaperonin complex component, TCP-1 zeta subunit (CCT6) [Posttranslational modification, protein turnover, chaperones]
Probab=34.86 E-value=48 Score=27.94 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=26.5
Q ss_pred CceeeEEeecCCCcceeEEEEecCC-cchH
Q 034762 15 GTKKVSYERDTKIINAASFTIEREE-HTIG 43 (84)
Q Consensus 15 ge~Ki~~~~~~~~~n~~~~~i~~Ed-HTLg 43 (84)
||.|.+.+++.+.++++++.|+|-. ||+-
T Consensus 348 GEEkfTFIE~~~~p~S~TiLikgpnkht~t 377 (520)
T KOG0359|consen 348 GEEKFTFIEKCNNPSSVTILIKGPNKHTIT 377 (520)
T ss_pred cceeeEeeecCCCCcceEEEEeCCccchHH
Confidence 7999999999999999999999987 8865
No 35
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=33.23 E-value=71 Score=25.01 Aligned_cols=38 Identities=16% Similarity=0.183 Sum_probs=30.4
Q ss_pred ceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhc-CCc
Q 034762 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHR-DEN 55 (84)
Q Consensus 16 e~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~-~~~ 55 (84)
...|++..-+ ++.+.|++.+.|=...|.||..+.. .|-
T Consensus 5 ~p~v~I~Elt--~d~vkF~L~nTdlsvANsLRRV~iaEvPT 43 (285)
T KOG1522|consen 5 QPTVKIRELT--DDNVKFVLSNTDLSVANSLRRVMIAEVPT 43 (285)
T ss_pred CCceEEEecC--CCceEEEEecChHHHHHHHHHHHHhcCce
Confidence 3467776644 8889999999999999999998775 343
No 36
>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=32.20 E-value=1.7e+02 Score=21.03 Aligned_cols=33 Identities=24% Similarity=0.462 Sum_probs=25.3
Q ss_pred cceeEEEEecCCcchHHHHHHHHhcCCceeEEe
Q 034762 28 INAASFTIEREEHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 28 ~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAg 60 (84)
.+...+.-....+++..+|+..|..+|++.+.|
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 455666555678999999999999999998876
No 37
>PF05986 ADAM_spacer1: ADAM-TS Spacer 1; InterPro: IPR010294 This domain represents the Spacer-1 domain from the ADAM-TS family of metalloproteinases []. A cellular disintegrin and metalloproteinase (ADAM) is a family of genes with structural homology to the snake venom metalloproteinases and disintegrins []. There is variation amongst members of the family, however, all have a similar domain organisation comprising a preproregion, a reprolysin-type catalytic domain, a disintegrin-like domain, a thrombospondin type-1 (TS) module, a cysteine-rich domain, a spacer domain without cysteine residues, and a COOH-terminal TS module [, ]. They are involved in embryogenesis and have been implicated in some cancers and inflammatory diseases [].; GO: 0004222 metalloendopeptidase activity, 0031012 extracellular matrix
Probab=30.97 E-value=1.5e+02 Score=19.24 Aligned_cols=71 Identities=17% Similarity=0.197 Sum_probs=44.0
Q ss_pred cccceeeeCCCceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcCCceeEEe----e----------eCCCCCCcc
Q 034762 5 DRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG----Y----------KLPHPLQYK 70 (84)
Q Consensus 5 ~~~~~~~l~~ge~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAg----Y----------~vpHPl~~~ 70 (84)
+-.+.+.+|.|-+.|.+.+.....|.+.+.-.. ++-+.|-= +.+.....+.+|| | .++.|+...
T Consensus 15 gY~~v~~IP~GA~nI~I~e~~~s~n~Lalk~~~-g~y~lNg~-~~i~~~~~~~~aGt~~~Y~~~~~~~E~i~~~GPl~e~ 92 (114)
T PF05986_consen 15 GYNKVVTIPAGARNIRITERRPSSNYLALKNSD-GKYVLNGN-WVISWPGTYSVAGTTFEYSRSDDNLERITAPGPLTED 92 (114)
T ss_pred CceEEEECCCCceEEEEEEeecCccEEEEEecC-CcEEEcCC-ccccCCcCEEeCCeEEEEEecCCCCEEEEcCCCCCCC
Confidence 344678999999999999877666777666444 55555542 2222223345444 2 346687777
Q ss_pred eEEEEEe
Q 034762 71 IIVRAEL 77 (84)
Q Consensus 71 i~l~Iqt 77 (84)
+.+.|=.
T Consensus 93 l~v~vl~ 99 (114)
T PF05986_consen 93 LIVQVLS 99 (114)
T ss_pred EEEEEEE
Confidence 7766643
No 38
>TIGR02533 type_II_gspE general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
Probab=28.97 E-value=1.3e+02 Score=24.59 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=20.1
Q ss_pred CcchHHHHHHHHhcCCceeEEe
Q 034762 39 EHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 39 dHTLgNlLr~~Ll~~~~V~fAg 60 (84)
+-|+.++||..|..+|+|.+.|
T Consensus 297 g~~f~~~lr~~LR~dPDvI~vG 318 (486)
T TIGR02533 297 GLTFAAGLRAILRQDPDIIMVG 318 (486)
T ss_pred CccHHHHHHHHHhcCCCEEEEe
Confidence 4689999999999999999887
No 39
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=28.45 E-value=57 Score=26.14 Aligned_cols=36 Identities=19% Similarity=0.138 Sum_probs=28.9
Q ss_pred ceeeEEeecCCCcceeEEEEecCCcchHHHHHHHHhcC
Q 034762 16 TKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRD 53 (84)
Q Consensus 16 e~Ki~~~~~~~~~n~~~~~i~~EdHTLgNlLr~~Ll~~ 53 (84)
.-||.+.. ...+.++|-+.|-|-.+.|++|..|+..
T Consensus 45 ~~~V~iv~--~~~~~leFDligIda~IANAfRRILiaE 80 (338)
T KOG1521|consen 45 NFKVDIVS--LDEETLEFDLIGIDASIANAFRRILIAE 80 (338)
T ss_pred ceEEEEEe--ccCcceeEEEeeccHHHHHHHHHHHHhh
Confidence 34455555 4477999999999999999999999863
No 40
>COG0634 Hpt Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=27.42 E-value=74 Score=23.35 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=17.3
Q ss_pred EecCCcchHHHHHHHHhcCC
Q 034762 35 IEREEHTIGNILRMQLHRDE 54 (84)
Q Consensus 35 i~~EdHTLgNlLr~~Ll~~~ 54 (84)
|-++.|||..+.+....+.|
T Consensus 102 IiDsG~TLs~i~~~l~~r~a 121 (178)
T COG0634 102 IIDSGLTLSKVRDLLKERGA 121 (178)
T ss_pred ccccChhHHHHHHHHHhCCC
Confidence 67899999999999888865
No 41
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=25.43 E-value=2.6e+02 Score=20.69 Aligned_cols=29 Identities=21% Similarity=0.413 Sum_probs=23.0
Q ss_pred EEEEecC-CcchHHHHHHHHhcCCceeEEe
Q 034762 32 SFTIERE-EHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 32 ~~~i~~E-dHTLgNlLr~~Ll~~~~V~fAg 60 (84)
.+.+..+ +-|+..+|+..|..+|+|.+.|
T Consensus 127 q~~v~~~~~~~~~~~l~~~lR~~PD~i~vg 156 (264)
T cd01129 127 QVQVNEKAGLTFARGLRAILRQDPDIIMVG 156 (264)
T ss_pred EEEeCCcCCcCHHHHHHHHhccCCCEEEec
Confidence 3444443 4699999999999999999876
No 42
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
Probab=25.09 E-value=2.8e+02 Score=21.05 Aligned_cols=32 Identities=13% Similarity=0.330 Sum_probs=25.3
Q ss_pred cceeEEEEecCCc-chHHHHHHHHhcCCceeEEe
Q 034762 28 INAASFTIEREEH-TIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 28 ~n~~~~~i~~EdH-TLgNlLr~~Ll~~~~V~fAg 60 (84)
+|.+.+.. +++. |+..+|+..|..+|++.+.|
T Consensus 179 ~~~v~~~~-~~~~~~~~~~l~~aLR~~pD~iivG 211 (299)
T TIGR02782 179 PNVVQLRT-SDDAISMTRLLKATLRLRPDRIIVG 211 (299)
T ss_pred CCEEEEEe-cCCCCCHHHHHHHHhcCCCCEEEEe
Confidence 45555543 4555 99999999999999999877
No 43
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=23.95 E-value=1.2e+02 Score=17.11 Aligned_cols=31 Identities=10% Similarity=0.106 Sum_probs=23.8
Q ss_pred HHHHHHHhcCCceeEEeeeCCCCCCcceEEEEE
Q 034762 44 NILRMQLHRDENVLFAGYKLPHPLQYKIIVRAE 76 (84)
Q Consensus 44 NlLr~~Ll~~~~V~fAgY~vpHPl~~~i~l~Iq 76 (84)
+.++..|.++|.|.=|.-+-..| +.+.+.|+
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P--~~l~I~V~ 67 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFP--NTLEIKVK 67 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETT--TEEEEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCC--CEEEEEEE
Confidence 56778888999999888887777 55666654
No 44
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=22.80 E-value=2e+02 Score=18.08 Aligned_cols=36 Identities=17% Similarity=0.106 Sum_probs=23.8
Q ss_pred CcceeEEEEecCCcchHHHHHHHHhcCCceeEEeee
Q 034762 27 IINAASFTIEREEHTIGNILRMQLHRDENVLFAGYK 62 (84)
Q Consensus 27 ~~n~~~~~i~~EdHTLgNlLr~~Ll~~~~V~fAgY~ 62 (84)
.....++.+...+..-...|...|.+.++|.=.-+.
T Consensus 20 ~~~~~s~~f~~~~~a~~spLA~~Lf~i~gV~~Vf~~ 55 (87)
T PF08712_consen 20 LLPGGSFEFKSAEEASDSPLAQALFAIPGVKSVFIG 55 (87)
T ss_dssp SSTS---EEESSS-TTS-HHHHHHHTSTTEEEEEEE
T ss_pred eecCccEEeCChHHcccCHHHHHhcCCCCEeEEEEE
Confidence 334446778888888889999999999999855443
No 45
>PHA02781 hypothetical protein; Provisional
Probab=22.29 E-value=88 Score=19.77 Aligned_cols=27 Identities=30% Similarity=0.350 Sum_probs=22.2
Q ss_pred eeeEEeecCCCcceeEEEEecCCcchH
Q 034762 17 KKVSYERDTKIINAASFTIEREEHTIG 43 (84)
Q Consensus 17 ~Ki~~~~~~~~~n~~~~~i~~EdHTLg 43 (84)
.||++..+++..|-+++...-|--|+.
T Consensus 6 dkikitvdskignvvtisynlekitid 32 (78)
T PHA02781 6 DKIKITVDSKIGNVVTISYNLEKITID 32 (78)
T ss_pred ceEEEEeecccCcEEEEEeeeEEEEEe
Confidence 478888899999999998888877764
No 46
>PF04263 TPK_catalytic: Thiamin pyrophosphokinase, catalytic domain; InterPro: IPR007371 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0005524 ATP binding, 0009229 thiamine diphosphate biosynthetic process; PDB: 2F17_B 1IG3_B 3S4Y_B 2OMK_B 1IG0_A 3MEL_B 3CQ9_A 3LM8_B 3K94_B 3L8M_B ....
Probab=22.20 E-value=52 Score=22.01 Aligned_cols=15 Identities=20% Similarity=0.257 Sum_probs=10.5
Q ss_pred CCcchHHHHHHHHhc
Q 034762 38 EEHTIGNILRMQLHR 52 (84)
Q Consensus 38 EdHTLgNlLr~~Ll~ 52 (84)
-||||+|+..-.-.+
T Consensus 98 ~DH~lanl~~l~~~~ 112 (123)
T PF04263_consen 98 FDHTLANLNLLYKYK 112 (123)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 589999986544433
No 47
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=21.51 E-value=2.6e+02 Score=23.18 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=22.6
Q ss_pred EEEecC-CcchHHHHHHHHhcCCceeEEe
Q 034762 33 FTIERE-EHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 33 ~~i~~E-dHTLgNlLr~~Ll~~~~V~fAg 60 (84)
+.+..+ ..|+.++|+..|.++|+|.+.|
T Consensus 364 ~~v~~~~g~~~~~~l~~~LR~dPDvI~vG 392 (564)
T TIGR02538 364 VNVNPKIGLTFAAALRSFLRQDPDIIMVG 392 (564)
T ss_pred EEeccccCCCHHHHHHHHhccCCCEEEeC
Confidence 444433 3799999999999999999876
No 48
>PF01933 UPF0052: Uncharacterised protein family UPF0052; InterPro: IPR002882 This entry contains LPPG:Fo 2-phospho-L-lactate transferase (CofD) and related sequences of unknown function belong to unidentified protein family UPF0052. CofD catalyses the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) [] but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. ; PDB: 2HZB_A 2O2Z_C 3CGW_A 3C3E_D 3C3D_D 2PPV_A 2P0Y_A 2Q7X_B.
Probab=21.13 E-value=62 Score=24.96 Aligned_cols=15 Identities=27% Similarity=0.481 Sum_probs=10.8
Q ss_pred cCCcchHHHHHHHHh
Q 034762 37 REEHTIGNILRMQLH 51 (84)
Q Consensus 37 ~EdHTLgNlLr~~Ll 51 (84)
-.+|+|||+++..+.
T Consensus 84 l~~hslGNl~l~~~~ 98 (300)
T PF01933_consen 84 LAGHSLGNLFLTALL 98 (300)
T ss_dssp GTT-BHHHHHHHHHH
T ss_pred HhhCchhHHHHHHHH
Confidence 358999999996554
No 49
>PRK10436 hypothetical protein; Provisional
Probab=20.97 E-value=1.5e+02 Score=24.18 Aligned_cols=22 Identities=32% Similarity=0.555 Sum_probs=20.1
Q ss_pred CcchHHHHHHHHhcCCceeEEe
Q 034762 39 EHTIGNILRMQLHRDENVLFAG 60 (84)
Q Consensus 39 dHTLgNlLr~~Ll~~~~V~fAg 60 (84)
.-|+.++||..|.++|+|.+.|
T Consensus 273 g~~f~~~lr~~LR~dPDvI~vG 294 (462)
T PRK10436 273 GLTFQRVLRALLRQDPDVIMVG 294 (462)
T ss_pred CcCHHHHHHHHhcCCCCEEEEC
Confidence 3689999999999999999887
Done!