Query psy7583
Match_columns 451
No_of_seqs 181 out of 1443
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 22:08:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7583.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7583hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07225 DNA-directed RNA poly 100.0 2E-127 5E-132 1030.1 34.0 402 1-450 162-601 (605)
2 TIGR03670 rpoB_arch DNA-direct 100.0 7E-127 2E-131 1025.1 33.9 402 1-450 156-595 (599)
3 PRK08565 DNA-directed RNA poly 100.0 1E-118 2E-123 1021.7 31.7 402 1-450 660-1099(1103)
4 KOG0215|consensus 100.0 1E-120 2E-125 960.8 13.6 397 1-450 715-1148(1153)
5 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 2E-113 5E-118 960.8 30.7 392 1-449 435-866 (866)
6 COG0085 RpoB DNA-directed RNA 100.0 4E-112 8E-117 938.6 29.4 374 1-450 640-1056(1060)
7 KOG0214|consensus 100.0 6E-113 1E-117 911.7 14.6 405 1-451 700-1140(1141)
8 KOG0216|consensus 100.0 2E-107 5E-112 862.8 22.0 381 1-450 680-1110(1111)
9 PRK00405 rpoB DNA-directed RNA 100.0 2E-103 5E-108 891.8 30.3 374 13-449 675-1106(1112)
10 TIGR02013 rpoB DNA-directed RN 100.0 3E-103 7E-108 886.5 28.0 347 77-448 663-1065(1065)
11 CHL00207 rpoB RNA polymerase b 100.0 7E-102 2E-106 869.3 31.4 408 13-449 543-1051(1077)
12 CHL00001 rpoB RNA polymerase b 100.0 4E-100 9E-105 858.3 28.3 372 54-450 618-1057(1070)
13 PRK09603 bifunctional DNA-dire 100.0 3E-93 6.5E-98 829.3 29.2 371 54-450 773-1373(2890)
14 PRK14844 bifunctional DNA-dire 100.0 8.9E-88 1.9E-92 781.3 27.0 372 54-450 783-1431(2836)
15 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 5E-84 1.1E-88 667.5 22.8 310 1-357 29-386 (386)
16 PF04560 RNA_pol_Rpb2_7: RNA p 100.0 8.7E-32 1.9E-36 220.0 5.8 81 359-450 1-81 (81)
17 KOG0214|consensus 98.6 2.4E-09 5.2E-14 117.6 -2.6 310 74-404 728-1061(1141)
18 CHL00207 rpoB RNA polymerase b 98.3 2.7E-07 5.8E-12 106.2 2.8 62 21-82 615-686 (1077)
19 CHL00001 rpoB RNA polymerase b 98.1 1.3E-06 2.7E-11 101.1 2.0 66 15-82 605-691 (1070)
20 PRK07225 DNA-directed RNA poly 93.8 0.023 5E-07 62.8 0.9 38 42-82 206-243 (605)
21 TIGR03670 rpoB_arch DNA-direct 93.0 0.038 8.1E-07 61.1 0.9 38 42-82 200-237 (599)
22 PF00562 RNA_pol_Rpb2_6: RNA p 91.8 0.057 1.2E-06 56.7 0.5 46 36-81 71-116 (386)
23 cd00653 RNA_pol_B_RPB2 RNA pol 89.8 0.15 3.2E-06 59.0 1.4 37 43-82 480-516 (866)
24 PRK14844 bifunctional DNA-dire 89.2 0.28 6.1E-06 61.6 3.3 56 21-76 785-850 (2836)
25 PRK08565 DNA-directed RNA poly 89.0 0.097 2.1E-06 61.9 -0.7 38 42-82 704-741 (1103)
26 TIGR02013 rpoB DNA-directed RN 87.8 0.25 5.5E-06 58.2 1.6 78 5-82 607-713 (1065)
27 PRK00405 rpoB DNA-directed RNA 87.8 0.27 5.8E-06 58.3 1.8 47 36-82 709-755 (1112)
28 PRK09603 bifunctional DNA-dire 79.7 1.3 2.9E-05 56.1 3.0 53 21-73 775-837 (2890)
29 COG0085 RpoB DNA-directed RNA 79.5 2 4.2E-05 50.4 4.1 72 17-92 566-678 (1060)
30 PRK00398 rpoP DNA-directed RNA 78.6 2.2 4.9E-05 30.9 2.8 27 393-419 3-29 (46)
31 KOG0215|consensus 77.7 0.75 1.6E-05 51.9 0.1 47 32-81 749-795 (1153)
32 PF04941 LEF-8: Late expressio 75.6 5.2 0.00011 44.8 5.8 54 206-259 681-735 (748)
33 PHA03394 lef-8 DNA-directed RN 75.5 6.1 0.00013 44.9 6.4 54 207-260 672-726 (865)
34 cd00350 rubredoxin_like Rubred 75.2 1.7 3.7E-05 29.4 1.3 26 393-420 1-26 (33)
35 PF09082 DUF1922: Domain of un 75.0 2.6 5.6E-05 33.6 2.4 49 391-441 1-55 (68)
36 PF12760 Zn_Tnp_IS1595: Transp 73.5 4.3 9.4E-05 29.5 3.2 37 378-419 8-45 (46)
37 COG1997 RPL43A Ribosomal prote 71.9 2.5 5.5E-05 35.2 1.8 28 392-419 34-61 (89)
38 PRK14890 putative Zn-ribbon RN 70.5 2 4.4E-05 33.2 0.9 31 389-419 3-33 (59)
39 cd00729 rubredoxin_SM Rubredox 68.6 3.3 7.2E-05 28.4 1.5 26 393-420 2-27 (34)
40 PF07754 DUF1610: Domain of un 67.7 3.2 7E-05 26.4 1.2 23 396-418 1-23 (24)
41 COG1645 Uncharacterized Zn-fin 64.0 5.4 0.00012 35.8 2.4 24 394-419 29-52 (131)
42 COG1592 Rubrerythrin [Energy p 61.7 3.8 8.1E-05 38.3 1.0 24 393-419 134-157 (166)
43 KOG0216|consensus 60.4 3.7 8E-05 46.8 0.8 34 38-74 720-753 (1111)
44 PF08792 A2L_zn_ribbon: A2L zi 58.2 10 0.00022 25.9 2.4 27 393-419 3-29 (33)
45 smart00661 RPOL9 RNA polymeras 58.0 6.5 0.00014 28.8 1.6 25 395-419 2-28 (52)
46 PF01780 Ribosomal_L37ae: Ribo 57.9 9.1 0.0002 32.2 2.6 29 391-419 33-61 (90)
47 PF08271 TF_Zn_Ribbon: TFIIB z 57.8 11 0.00024 26.9 2.7 25 394-418 1-26 (43)
48 COG1096 Predicted RNA-binding 56.5 8.3 0.00018 36.6 2.4 35 394-431 150-184 (188)
49 PRK06266 transcription initiat 55.5 7.1 0.00015 36.8 1.7 45 374-419 99-144 (178)
50 COG1996 RPC10 DNA-directed RNA 52.6 11 0.00024 28.1 2.0 29 391-419 4-32 (49)
51 PF07295 DUF1451: Protein of u 52.1 10 0.00023 34.6 2.2 28 393-420 112-139 (146)
52 COG1545 Predicted nucleic-acid 50.8 9.4 0.0002 34.5 1.7 37 389-429 25-61 (140)
53 PRK00420 hypothetical protein; 49.4 11 0.00023 33.0 1.8 25 394-419 24-48 (112)
54 COG2401 ABC-type ATPase fused 47.4 6.7 0.00015 42.0 0.2 54 382-440 117-174 (593)
55 smart00531 TFIIE Transcription 46.9 12 0.00027 33.8 1.8 42 377-419 84-131 (147)
56 PRK11032 hypothetical protein; 46.4 16 0.00034 34.0 2.4 28 393-420 124-151 (160)
57 smart00659 RPOLCX RNA polymera 46.2 19 0.00042 26.1 2.4 26 393-419 2-27 (44)
58 TIGR00373 conserved hypothetic 45.8 12 0.00025 34.6 1.5 45 374-419 91-136 (158)
59 TIGR00280 L37a ribosomal prote 45.0 13 0.00028 31.4 1.5 29 391-419 33-61 (91)
60 PF02150 RNA_POL_M_15KD: RNA p 44.5 16 0.00035 25.1 1.7 26 394-419 2-28 (35)
61 PF11781 RRN7: RNA polymerase 44.5 17 0.00036 25.3 1.8 24 395-419 10-33 (36)
62 PF06677 Auto_anti-p27: Sjogre 44.1 19 0.0004 25.9 2.0 24 394-418 18-41 (41)
63 COG2888 Predicted Zn-ribbon RN 40.7 19 0.0004 28.1 1.7 27 393-419 9-35 (61)
64 PRK03976 rpl37ae 50S ribosomal 40.4 17 0.00036 30.7 1.5 29 391-419 34-62 (90)
65 PTZ00255 60S ribosomal protein 40.2 16 0.00034 30.8 1.3 30 390-419 33-62 (90)
66 PF09538 FYDLN_acid: Protein o 39.4 14 0.00029 32.2 0.9 28 392-420 8-35 (108)
67 TIGR01053 LSD1 zinc finger dom 39.3 23 0.00049 23.9 1.7 25 395-419 3-27 (31)
68 COG0266 Nei Formamidopyrimidin 38.1 22 0.00048 35.8 2.3 24 395-418 247-272 (273)
69 PF07282 OrfB_Zn_ribbon: Putat 34.9 20 0.00044 27.8 1.1 28 392-419 27-54 (69)
70 PF09297 zf-NADH-PPase: NADH p 34.1 41 0.00089 22.4 2.4 25 394-418 4-28 (32)
71 PF04810 zf-Sec23_Sec24: Sec23 34.1 21 0.00046 25.2 1.0 27 394-420 3-33 (40)
72 COG3357 Predicted transcriptio 33.7 15 0.00033 30.9 0.3 26 394-419 59-84 (97)
73 PF03604 DNA_RNApol_7kD: DNA d 32.0 28 0.00062 23.6 1.3 25 394-419 1-25 (32)
74 KOG3507|consensus 31.9 33 0.00071 26.7 1.8 26 392-418 19-44 (62)
75 PRK13130 H/ACA RNA-protein com 31.1 35 0.00075 26.2 1.8 24 392-421 4-27 (56)
76 TIGR02300 FYDLN_acid conserved 31.0 24 0.00052 31.6 1.0 28 392-420 8-35 (129)
77 PF14353 CpXC: CpXC protein 28.8 16 0.00034 32.1 -0.5 40 364-405 11-50 (128)
78 PRK11788 tetratricopeptide rep 28.4 39 0.00086 34.2 2.3 31 387-423 350-380 (389)
79 smart00834 CxxC_CXXC_SSSS Puta 28.0 50 0.0011 22.7 2.1 27 393-419 5-34 (41)
80 PF05191 ADK_lid: Adenylate ki 27.9 34 0.00074 23.8 1.2 26 394-419 2-29 (36)
81 PF14803 Nudix_N_2: Nudix N-te 27.9 53 0.0012 22.6 2.1 24 395-418 2-29 (34)
82 PF13533 Biotin_lipoyl_2: Biot 27.2 45 0.00097 24.4 1.8 15 166-180 17-31 (50)
83 PF12172 DUF35_N: Rubredoxin-l 26.8 56 0.0012 22.3 2.1 25 391-419 9-33 (37)
84 COG2956 Predicted N-acetylgluc 26.7 38 0.00083 35.2 1.8 41 379-427 344-384 (389)
85 COG2260 Predicted Zn-ribbon RN 26.4 38 0.00082 26.3 1.3 25 393-423 5-29 (59)
86 PHA00626 hypothetical protein 25.9 53 0.0012 25.3 2.0 24 395-418 2-30 (59)
87 COG0777 AccD Acetyl-CoA carbox 25.5 23 0.00049 35.8 -0.1 26 394-419 29-55 (294)
88 PF09723 Zn-ribbon_8: Zinc rib 25.2 71 0.0015 22.7 2.5 27 393-419 5-34 (42)
89 TIGR00416 sms DNA repair prote 24.7 47 0.001 35.8 2.2 29 391-423 5-33 (454)
90 PF13248 zf-ribbon_3: zinc-rib 24.7 34 0.00074 21.8 0.7 22 394-419 3-24 (26)
91 PRK14810 formamidopyrimidine-D 24.2 54 0.0012 32.8 2.3 24 395-418 246-271 (272)
92 PRK00432 30S ribosomal protein 23.9 44 0.00094 25.0 1.2 24 393-418 20-44 (50)
93 PF13408 Zn_ribbon_recom: Reco 23.8 1.3E+02 0.0028 21.9 3.9 46 394-439 6-57 (58)
94 TIGR02605 CxxC_CxxC_SSSS putat 23.4 81 0.0018 23.0 2.6 27 393-419 5-34 (52)
95 KOG0402|consensus 23.1 26 0.00056 29.1 -0.2 49 393-441 36-88 (92)
96 PRK10445 endonuclease VIII; Pr 23.1 58 0.0013 32.4 2.3 24 395-418 237-262 (263)
97 PRK12495 hypothetical protein; 22.6 41 0.00088 32.9 1.0 31 387-419 36-66 (226)
98 COG2835 Uncharacterized conser 21.9 93 0.002 24.3 2.7 30 391-420 6-35 (60)
99 PRK01103 formamidopyrimidine/5 21.9 67 0.0014 32.1 2.5 25 395-419 247-273 (274)
100 PRK11823 DNA repair protein Ra 21.7 59 0.0013 34.9 2.2 29 391-423 5-33 (446)
101 PRK14811 formamidopyrimidine-D 21.6 64 0.0014 32.3 2.2 26 395-420 237-264 (269)
102 KOG0703|consensus 21.0 75 0.0016 32.3 2.6 61 379-443 15-85 (287)
103 PF00799 Gemini_AL1: Geminivir 20.9 37 0.00081 29.7 0.4 25 11-35 2-26 (114)
104 TIGR01384 TFS_arch transcripti 20.5 55 0.0012 27.5 1.3 24 395-420 2-25 (104)
105 COG1594 RPB9 DNA-directed RNA 20.1 82 0.0018 27.5 2.3 28 394-421 3-32 (113)
106 PRK13945 formamidopyrimidine-D 20.0 72 0.0016 32.0 2.3 24 395-418 256-281 (282)
No 1
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=2.2e-127 Score=1030.05 Aligned_cols=402 Identities=47% Similarity=0.804 Sum_probs=372.4
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||+|++|++.|+|+++|+|+|||+|||+|+++++++++++|+|+||+|||
T Consensus 162 ~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAv------------------------------ 211 (605)
T PRK07225 162 LGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAV------------------------------ 211 (605)
T ss_pred cCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEE------------------------------
Confidence 89999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCc-hhhhh
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMR-NAIYD 159 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~-~~~~~ 159 (451)
|||+||||||||||||+|+|||||||+||++|+.++++...+.++.|++|+.+. .+.+ ...|+
T Consensus 212 ---------------msy~GYn~EDAiIiNkssidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~~-~~~~~~~~~~ 275 (605)
T PRK07225 212 ---------------MSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEEAYR 275 (605)
T ss_pred ---------------ECcCCCChhHeeeeehhhhhcCceEEEEEEEEEEEeeecCCCcceEEecCCchh-ccccChHHhh
Confidence 999999999999999999999999999999999998887777778999987531 1222 35799
Q ss_pred ccCcCCCcccCcEEeCCCEEEEEeeecCCCCcc-ccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEee
Q psy7583 160 KLDDDGIIAPGLRVSGDDVVIGKTITLPENEDE-LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRS 238 (451)
Q Consensus 160 ~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~-~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~ 238 (451)
+||+||||+||++|++|||||||++|....++. ..+ ......+|+|++++.+|+|+||+|.++.+.+|.+.+||++|+
T Consensus 276 ~LD~dGi~~~G~~v~~gdiligk~sp~~~~~~~~~~~-~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~ 354 (605)
T PRK07225 276 HLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFG-ISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRD 354 (605)
T ss_pred cCCCCCCccCCCEECCCCEEEEEecCCCCccchhhhc-ccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEE
Confidence 999999999999999999999999986532111 001 111247899999999999999999999999999999999999
Q ss_pred cCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCc
Q psy7583 239 VRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDA 282 (451)
Q Consensus 239 ~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~ 282 (451)
.|+|+||||||||||||||||+||||| ++++.|.+.|+|||...
T Consensus 355 ~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~ 434 (605)
T PRK07225 355 LRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGE 434 (605)
T ss_pred EEeccccchhhhcccCceeEEeEeccccCCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCc
Confidence 999999999999999999999999999 57889999999999987
Q ss_pred ccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccc
Q psy7583 283 VNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLR 362 (451)
Q Consensus 283 ~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r 362 (451)
+.+++++.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++||||
T Consensus 435 -~~~~~~~~L~~~g~~~~G~e~my~G~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~R 513 (605)
T PRK07225 435 -DEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLR 513 (605)
T ss_pred -hHHHHHHHHHHhCcCCCCeEEEEcCCCCCEecccEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCee
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhC
Q psy7583 363 FGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSM 442 (451)
Q Consensus 363 ~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm 442 (451)
|||||+|||+||||+++|+|||+++||.++++||.+||++++.+.+.+.+.|+.|+++..+.++.+|||||||+|||+||
T Consensus 514 fGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL~sm 593 (605)
T PRK07225 514 FGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSL 593 (605)
T ss_pred eeeeehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCcceehhcccCceeecccCCCCceeeccCChhHHHHHHHHHHC
Confidence 99999999999999999999999999999999999999999877666778899999888999999999999999999999
Q ss_pred CcccEEEE
Q psy7583 443 NIAPRLMV 450 (451)
Q Consensus 443 ~I~~r~~~ 450 (451)
||++||.+
T Consensus 594 ~i~~~l~~ 601 (605)
T PRK07225 594 GIAPRLEL 601 (605)
T ss_pred CceeEEEe
Confidence 99999976
No 2
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=100.00 E-value=7.4e-127 Score=1025.06 Aligned_cols=402 Identities=48% Similarity=0.838 Sum_probs=371.5
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||+|++|++.|+||++|+|+|||+|||+|+++++++++++|+|+||+|||
T Consensus 156 mG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAv------------------------------ 205 (599)
T TIGR03670 156 LGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAV------------------------------ 205 (599)
T ss_pred ccccccChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCeeEEEEE------------------------------
Confidence 89999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCc-hhhhh
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMR-NAIYD 159 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~-~~~~~ 159 (451)
|||+||||||||||||+|+|||||||+||++|+.++++...+.++.+++|+.. ..+.+ ...|+
T Consensus 206 ---------------msy~GYn~EDAiIink~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~-~~~~~~~~~~~ 269 (599)
T TIGR03670 206 ---------------MSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRGEEAYK 269 (599)
T ss_pred ---------------EcccCcChhHeeeechhhhhcCCeEEEEEEEEEEEeeccCCCCceEEecCCch-hccccchhhhc
Confidence 99999999999999999999999999999999998887766667788888653 22222 34699
Q ss_pred ccCcCCCcccCcEEeCCCEEEEEeeecCCCCc-cccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEee
Q psy7583 160 KLDDDGIIAPGLRVSGDDVVIGKTITLPENED-ELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRS 238 (451)
Q Consensus 160 ~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~-~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~ 238 (451)
+||+||||++|++|++|||||||++|....+. ...+ .+....+|.|++++.+|+|+||+|.++.+.++.+.+||++|+
T Consensus 270 ~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~~~~~~-~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~ 348 (599)
T TIGR03670 270 HLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELRELG-LVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRD 348 (599)
T ss_pred cCCCCCCcCCCcEeCCCCEEEEEecCCCCccchhhhc-cccccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEee
Confidence 99999999999999999999999998643211 0000 011246899999999999999999999999999999999999
Q ss_pred cCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCc
Q psy7583 239 VRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDA 282 (451)
Q Consensus 239 ~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~ 282 (451)
.|+|+||||||||||||||||+||||| ++++.|.+.|+|||.+.
T Consensus 349 ~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~d~t~F~~~ 428 (599)
T TIGR03670 349 LRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGE 428 (599)
T ss_pred eecCcchhhhhhhccCcceEEeEeccCCCCcCCCCCCCCEEECcccccccccHHHHHHHHHHHHHHhcCCEEEeCCCCCc
Confidence 999999999999999999999999999 56789999999999987
Q ss_pred ccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccc
Q psy7583 283 VNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLR 362 (451)
Q Consensus 283 ~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r 362 (451)
+.+++++.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++||||
T Consensus 429 -~~~~~~~~L~~~g~~~~G~e~ly~G~TG~~~~~~if~G~~yyqrL~HmV~DK~h~Rs~Gp~~~lTrQP~~Gr~r~GG~R 507 (599)
T TIGR03670 429 -PEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLR 507 (599)
T ss_pred -cHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEEEEehhheechhhhcchhhhcccCCCcccccCCccccccCCCee
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhC
Q psy7583 363 FGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSM 442 (451)
Q Consensus 363 ~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm 442 (451)
|||||+|||+||||+++|+|||+++||.+.++||.+||++++.+.+.+.+.|+.|+++.++..+.+|||||||+|||+||
T Consensus 508 fGEMErd~lia~Gas~~L~ErL~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~i~~v~iPy~~k~l~~EL~am 587 (599)
T TIGR03670 508 FGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSL 587 (599)
T ss_pred eeeeehhhHhhcchHHHHHHHHhccCcceeEEeecccCceeehhcccCceeccccCCCCceeeecCChhHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999877666778899999988999999999999999999999
Q ss_pred CcccEEEE
Q psy7583 443 NIAPRLMV 450 (451)
Q Consensus 443 ~I~~r~~~ 450 (451)
||++||.+
T Consensus 588 ~i~~~l~~ 595 (599)
T TIGR03670 588 GISPRLEL 595 (599)
T ss_pred CcceEEEe
Confidence 99999976
No 3
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=1.1e-118 Score=1021.66 Aligned_cols=402 Identities=51% Similarity=0.865 Sum_probs=370.1
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||++++|++.|+|+++|+|+|||+|||+|++++.++++++|+|+||+|||
T Consensus 660 ~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv------------------------------ 709 (1103)
T PRK08565 660 LGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAV------------------------------ 709 (1103)
T ss_pred cccccccceEeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEE------------------------------
Confidence 79999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCc-hhhhh
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMR-NAIYD 159 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~-~~~~~ 159 (451)
|||+||||||||||||+|+|||||||+||++|++++++...+.++.|+.|.+. ..+.+ ...|+
T Consensus 710 ---------------~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 773 (1103)
T PRK08565 710 ---------------LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPN-VRGYRGEEYYR 773 (1103)
T ss_pred ---------------EcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeecCCCCceEEecCCCc-ccccCchhhhh
Confidence 99999999999999999999999999999999998877655666778887542 22222 34689
Q ss_pred ccCcCCCcccCcEEeCCCEEEEEeeecCCCCc-cccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEee
Q psy7583 160 KLDDDGIIAPGLRVSGDDVVIGKTITLPENED-ELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRS 238 (451)
Q Consensus 160 ~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~-~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~ 238 (451)
+||+||||+||++|++|||||||++|.....+ .+.+ ....+.+|+|++++.+|+|+||+|.++.+.++.+.|||++|+
T Consensus 774 ~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~-~~~~~~~~~s~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~ 852 (1103)
T PRK08565 774 KLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELS-LGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRD 852 (1103)
T ss_pred cCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhcc-ccCCccccceEEecCCCceEEEEEEEEecCCCcEEEEEEEEE
Confidence 99999999999999999999999998642211 1111 111247899999999999999999999999999999999999
Q ss_pred cCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCc
Q psy7583 239 VRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDA 282 (451)
Q Consensus 239 ~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~ 282 (451)
.|+|+||||||||||||||||+||||| ++++.|.+.|+|||...
T Consensus 853 ~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~d~t~F~~~ 932 (1103)
T PRK08565 853 LRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGE 932 (1103)
T ss_pred EecCchhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhcCceeeecCcCCc
Confidence 999999999999999999999999999 56789999999999987
Q ss_pred ccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccc
Q psy7583 283 VNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLR 362 (451)
Q Consensus 283 ~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r 362 (451)
..+++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++||||
T Consensus 933 -~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~R~~Gp~~~lt~QP~~Gr~~~GG~R 1011 (1103)
T PRK08565 933 -PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLR 1011 (1103)
T ss_pred -hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhhccCCCcchhhhCCccccccCCCee
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhC
Q psy7583 363 FGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSM 442 (451)
Q Consensus 363 ~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm 442 (451)
|||||+|||+||||+++|+|||+++||.++++||.+||++++.+.+++.+.|+.|+++..+..+.+|||||||+|||+||
T Consensus 1012 ~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~~~~~~~~v~iPy~~k~l~~EL~sm 1091 (1103)
T PRK08565 1012 FGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSM 1091 (1103)
T ss_pred eecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccCCCCcceeccCChhHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999877777788999999888899999999999999999999
Q ss_pred CcccEEEE
Q psy7583 443 NIAPRLMV 450 (451)
Q Consensus 443 ~I~~r~~~ 450 (451)
||++||.|
T Consensus 1092 ~i~~~l~~ 1099 (1103)
T PRK08565 1092 GISPRLKL 1099 (1103)
T ss_pred CCceEEEe
Confidence 99999976
No 4
>KOG0215|consensus
Probab=100.00 E-value=1.1e-120 Score=960.84 Aligned_cols=397 Identities=40% Similarity=0.714 Sum_probs=371.6
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||.++||+..|.||.+|.|.|||+|+|+||++|+++||++||||||.|||
T Consensus 715 mG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAV------------------------------ 764 (1153)
T KOG0215|consen 715 MGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAV------------------------------ 764 (1153)
T ss_pred hhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEE------------------------------
Confidence 79999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCchhhhhc
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDK 160 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~~~~~~~ 160 (451)
|||+|||+|||+|+||+|+||||+|+.+||+.+...+++.++..+++..|-.+...+..-...+.
T Consensus 765 ---------------MSYSGYDIEDALVLNKsSlDRGfGRC~Vyk~~~~~~kkY~N~T~Drimgp~~d~~t~kpi~kh~v 829 (1153)
T KOG0215|consen 765 ---------------MSYSGYDIEDALVLNKSSIDRGFGRCEVYKKTTTTLKKYANGTFDRIMGPQLDPNTRKPIWKHQV 829 (1153)
T ss_pred ---------------EeccCCchhhhhhcccchhccCcceEEEEeeeeeeeeecCCCchhhhcccccCCCcCCcchhhcc
Confidence 99999999999999999999999999999999999999999888888877655433334456778
Q ss_pred cCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccc-cccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEeec
Q psy7583 161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTT-KRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV 239 (451)
Q Consensus 161 LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~-~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~ 239 (451)
||+|||..||..|++|+|+|+|-.|..+.. ++.+.+ ....|++.++.||..|+++||+|.++.+.++...+|+.+||+
T Consensus 830 Ld~DGl~~pG~~V~~~qi~iNK~mP~vt~~-~~~~~~~~~~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQT 908 (1153)
T KOG0215|consen 830 LDDDGLATPGERVQPGQIYINKQMPTVTGT-SLPGLSASQVQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQT 908 (1153)
T ss_pred cCcccCCCCccEeccCcEEEeccCCCcccc-cCCCCCccccccccccceecCCCcchhheeEeecCccccHHHHHHHhhc
Confidence 999999999999999999999988876543 232222 223589999999999999999999999988888999999999
Q ss_pred CCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCcc
Q psy7583 240 RIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDAV 283 (451)
Q Consensus 240 R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~~ 283 (451)
|+||+|||||||||||||||.|++|| +|.+.|+|.++|+|.+.
T Consensus 909 RrPElGDKFSSRHGQKGVcGlIv~QEDMPFnD~GIcPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~hYGTaFGgs- 987 (1153)
T KOG0215|consen 909 RRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFHYGTAFGGS- 987 (1153)
T ss_pred cCcccccccccccCCCceeeEEeeccCCCCcccCCCcccccCCCCCcccchHHHHHHHhccccceeeeeEeeccccCCc-
Confidence 99999999999999999999999999 57889999999999998
Q ss_pred cHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCcccc
Q psy7583 284 NVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRF 363 (451)
Q Consensus 284 ~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~ 363 (451)
+++++++.|.++|||+.||+.+|+|+|||+++|+||+||+|||||+|||.||||||++||+..|||||++||+|+||+|+
T Consensus 988 kVed~~~~Lv~hGfnY~GKD~ltSGITGepLeAYIffGPiYYQKLKHMVlDKMHARARGPRAvLTRQPTEGRSrdGGLRL 1067 (1153)
T KOG0215|consen 988 KVEDISEELVEHGFNYSGKDMLTSGITGEPLEAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRL 1067 (1153)
T ss_pred hHHHHHHHHHHhccCccCccccccCCCCCcceeeEEechHHHHHHHHHHHHHHhhhccCCceeeecCCCCCcCCCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhCC
Q psy7583 364 GEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMN 443 (451)
Q Consensus 364 GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm~ 443 (451)
||||||||+++||+.+|-|||+.+||.+++.||..||.+++.. +|..|++..++.++.||||||||||||+|||
T Consensus 1068 GEMERDCLIaYGASmLl~ERLMiSSDaFeVdVC~~CGllgykg------wC~~Ckss~~v~~~~iPYAcKLLFQEL~SMN 1141 (1153)
T KOG0215|consen 1068 GEMERDCLIAYGASMLLLERLMISSDAFEVDVCRQCGLLGYKG------WCTTCKSSKNVAKMKIPYACKLLFQELQSMN 1141 (1153)
T ss_pred chhhhhhhhhccHHHHHHHHHhhcCcceeeeeccccccceech------hhhhccCCCceeeeeccHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999998743 5999999999999999999999999999999
Q ss_pred cccEEEE
Q psy7583 444 IAPRLMV 450 (451)
Q Consensus 444 I~~r~~~ 450 (451)
|-|||.+
T Consensus 1142 i~PrL~L 1148 (1153)
T KOG0215|consen 1142 IVPRLKL 1148 (1153)
T ss_pred ccceeee
Confidence 9999976
No 5
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=2.1e-113 Score=960.75 Aligned_cols=392 Identities=49% Similarity=0.778 Sum_probs=359.0
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||+|++|++.|+|+++|+|+|||+|||+|++++.++++++|+|+||+|||
T Consensus 435 ~g~~~~n~~~r~d~~~~~l~~pq~plv~T~~~~~~~~~~~~~G~N~~VAv------------------------------ 484 (866)
T cd00653 435 VGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAV------------------------------ 484 (866)
T ss_pred cCchhccccccccchheeeccCCCCccccchHHHhCCCccCCCceEEEEE------------------------------
Confidence 79999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCchhhhhc
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDK 160 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~~~~~~~ 160 (451)
|||+||||||||||||+|+|||||||+||++|++++++...+.++.+. +. .+..+...|++
T Consensus 485 ---------------~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~~~~~~~-~~---~~~~~~~~~~~ 545 (866)
T cd00653 485 ---------------MSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GD---IPNVSEEKLKN 545 (866)
T ss_pred ---------------eccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCCcceEec-CC---CCCCChHHhhc
Confidence 999999999999999999999999999999999998876666555444 11 12234568999
Q ss_pred cCcCCCcccCcEEeCCCEEEEEeeecCCCCccc-cccccccccceeeEEecCCcceEEEEEEEEe---ccCCeeEEEEEE
Q psy7583 161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL-EGTTKRFSKRDGSTFLRNSETGIVDQVMLTL---NVDGYKFCKIRV 236 (451)
Q Consensus 161 LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~-~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~---~~~g~~~vkv~i 236 (451)
||+||||++|++|++||+||||++|....+... ... .....+|.|++++.+|+|+||+|.++. +.++...++|++
T Consensus 546 ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~~~~v~v~~ 624 (866)
T cd00653 546 LDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGE-KARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYI 624 (866)
T ss_pred cCCCCCcCCCCEecCCCEEEEEecCcccccccccccc-cCCcceEEEEEecCCCceEEEEEEEeccccCCCCcEEEEEEE
Confidence 999999999999999999999998864322110 111 112468999999999999999999988 577888999999
Q ss_pred eecCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCC
Q psy7583 237 RSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFN 280 (451)
Q Consensus 237 r~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~ 280 (451)
|+.|+|+||||||||||||||||+|||+| ++++.|.+.|+|||.
T Consensus 625 r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~t~f~ 704 (866)
T cd00653 625 RQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFD 704 (866)
T ss_pred eEEecCCcccccccccCCCcEEEEEeccccCCcccCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhcCCcccccccC
Confidence 99999999999999999999999999998 568899999999999
Q ss_pred CcccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCc
Q psy7583 281 DAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGG 360 (451)
Q Consensus 281 ~~~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg 360 (451)
.. ..+++.+.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++||
T Consensus 705 ~~-~~~~~~~~l~~~g~~~~G~e~~y~g~tG~~~~~~if~G~~yyqrL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG 783 (866)
T cd00653 705 GA-EEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGG 783 (866)
T ss_pred cc-hHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhhhhhhhhhchhhhhcccCCcchhccCcCccccccCC
Confidence 87 88999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHH
Q psy7583 361 LRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELM 440 (451)
Q Consensus 361 ~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~ 440 (451)
|||||||+|||+||||+++|+|||+++||++.++||.+||++++.. .|+.|+++.++..+.+|||||||+|||+
T Consensus 784 ~R~GEMErd~lia~Gas~~l~erl~~~SD~~~~~vc~~cg~i~~~~------~c~~c~~~~~~~~~~ipy~~kll~~EL~ 857 (866)
T cd00653 784 QRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYAFKLLFQELQ 857 (866)
T ss_pred eEEEEEehhhhhhhhhHHHHHHHHhcCCccceEEEeccCccccccc------ccccccCCCceeecCCCHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999998643 2999999999999999999999999999
Q ss_pred hCCcccEEE
Q psy7583 441 SMNIAPRLM 449 (451)
Q Consensus 441 sm~I~~r~~ 449 (451)
||||++||.
T Consensus 858 sm~i~~~~~ 866 (866)
T cd00653 858 SMNIDPRLK 866 (866)
T ss_pred HCCcceEeC
Confidence 999999973
No 6
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=3.8e-112 Score=938.55 Aligned_cols=374 Identities=39% Similarity=0.568 Sum_probs=350.4
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
+|++..|+..|.|+..|.++|||.|+|+| +++|+|||++||+
T Consensus 640 ~~~~~~~~~~~~d~~~~~~~~~~~P~~~~--------~e~~~GqN~~VA~------------------------------ 681 (1060)
T COG0085 640 TGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAF------------------------------ 681 (1060)
T ss_pred cCCCcccceeccccccccceecCCCcccc--------CcccCCceeEEEE------------------------------
Confidence 68999999999999999999999999999 8999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCchhhhhc
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDK 160 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~~~~~~~ 160 (451)
|||+|||+||||||||++++||+|||+||++|+.++++++.+.++.+++|+.. +..|++
T Consensus 682 ---------------m~~~GYn~EDAiiin~~~v~~~~~ts~~~~~~~~~~r~~~~g~e~~~~iP~~~------e~~~~~ 740 (1060)
T COG0085 682 ---------------MPWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVS------EEALRN 740 (1060)
T ss_pred ---------------ecccCcChhHheecccchhhcCCceEEEEEEEeeeeeccCCCccccccCCCcC------HHHHhc
Confidence 99999999999999999999999999999999999999999999999999764 568999
Q ss_pred cCcCCCcccCcEEeCCCEEEEEeeecCCCCcccccc---ccccccceeeEEecCCcceEEEEEEEEeccC----CeeEEE
Q psy7583 161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGT---TKRFSKRDGSTFLRNSETGIVDQVMLTLNVD----GYKFCK 233 (451)
Q Consensus 161 LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~---~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~----g~~~vk 233 (451)
||+|||++||++|++|||||||++|..+.+.+.+.. .--.+.+|+|++++++|+|+||+|.++.+.+ +++.||
T Consensus 741 Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~~ek~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vk 820 (1060)
T COG0085 741 LDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVK 820 (1060)
T ss_pred CCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccccceeeccceeecCCCCeEEEEEEEEeccCCCcCceEEEE
Confidence 999999999999999999999999987543211100 1011478999999999999999999999877 889999
Q ss_pred EEEeecCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeec
Q psy7583 234 IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDAT 277 (451)
Q Consensus 234 v~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~t 277 (451)
|++|+.|.|++|||||||||||||||+|||+| +|++.|...|+|
T Consensus 821 V~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~~~G~~~DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~~~~ 900 (1060)
T COG0085 821 VYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTP 900 (1060)
T ss_pred EEEEEeccCCccccccccCCCCceeeeecCcccCCcCCCCCcccEEECCCCCCccccHHHHHHHHHHHHHHhcCceeccC
Confidence 99999999999999999999999999999999 678899999999
Q ss_pred CCCCcccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccc
Q psy7583 278 PFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRAR 357 (451)
Q Consensus 278 pF~~~~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~ 357 (451)
||++. +.+++.++|.++||++.|++.||||+|||+|+++||||++|||||+|||+||+||||+||++.|||||++||++
T Consensus 901 ~F~g~-~~~~~~~~l~~~g~~~~Gk~~lydG~TGe~~~~~i~vG~~Y~~kL~HmV~dK~HaRs~GP~s~lT~QP~~Gka~ 979 (1060)
T COG0085 901 VFDGA-PEEDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHARSTGPYSLVTQQPLGGKAQ 979 (1060)
T ss_pred CcCCC-CHHHHHHHHHHcCCCCCCCEEeecCCCCCcccccEEEEehHHHhHHhhhcccceeeccCCceeeecCCCCcccc
Confidence 99997 99999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHH
Q psy7583 358 DGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQ 437 (451)
Q Consensus 358 ~Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~ 437 (451)
.|||||||||+|||+|||||++|+|||+.+||++ ||++++++ |+.|+ .++..+.||||||+|++
T Consensus 980 ~GG~RfGEME~~aL~ayGAa~~LqE~L~~~SD~~-------~G~~~~y~-------~~v~g--~~~~~~~ip~sFk~L~~ 1043 (1060)
T COG0085 980 FGGQRFGEMEVWALEAYGAAYTLQERLTVKSDDV-------CGRIKIYE-------CIVKG--ENIPEVGIPESFKVLLK 1043 (1060)
T ss_pred cCCccccchHHHHHHHHhHHHHHHHHhhccchhc-------ccchhhhc-------CcccC--CCCCCCCCCHHHHHHHH
Confidence 9999999999999999999999999999999999 99987764 99998 57899999999999999
Q ss_pred HHHhCCcccEEEE
Q psy7583 438 ELMSMNIAPRLMV 450 (451)
Q Consensus 438 EL~sm~I~~r~~~ 450 (451)
||+||||+|||.+
T Consensus 1044 El~sl~i~~~l~~ 1056 (1060)
T COG0085 1044 ELRSLGIDVRLEL 1056 (1060)
T ss_pred HHHHCCCceEEee
Confidence 9999999999975
No 7
>KOG0214|consensus
Probab=100.00 E-value=5.8e-113 Score=911.73 Aligned_cols=405 Identities=71% Similarity=1.123 Sum_probs=390.7
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||++.+|++.|+||..|+|+|||+|||+|++++++.|.++|+|+||+||+
T Consensus 700 mg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi------------------------------ 749 (1141)
T KOG0214|consen 700 MGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAI------------------------------ 749 (1141)
T ss_pred ceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEE------------------------------
Confidence 79999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCchhhhhc
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDK 160 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~~~~~~~ 160 (451)
++|+|||||||+|||++++|||||||.+|++|++++.+...+.++.|+.|....+.+++...|++
T Consensus 750 ---------------~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~~~~mr~~~~dk 814 (1141)
T KOG0214|consen 750 ---------------ACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGEGRGMRNGKYDK 814 (1141)
T ss_pred ---------------ecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhhhhccccccccccccccccccccccccccc
Confidence 99999999999999999999999999999999999988888889999999988888899999999
Q ss_pred cCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEeecC
Q psy7583 161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240 (451)
Q Consensus 161 LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~R 240 (451)
||+||++.||++|+.+||+|||.+|.++++++...+.+.+.++|.|+.++++|.|+||+|+++.|.+|++++||++|+.|
T Consensus 815 LdddG~i~~G~~vs~~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~~r 894 (1141)
T KOG0214|consen 815 LDDDGIIMPGSRVSGGDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQVR 894 (1141)
T ss_pred ccccCCccccceeecCCEEeccccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEeecc
Confidence 99999999999999999999999998888777777778889999999999999999999999999999999999999999
Q ss_pred CCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCccc
Q psy7583 241 IPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDAVN 284 (451)
Q Consensus 241 ~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~~~ 284 (451)
.|++|||||||||||||||.+++|| ++++.|...|+|||.+. .
T Consensus 895 ipqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a~~~e~~~atpFs~v-~ 973 (1141)
T KOG0214|consen 895 IPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAAYEGEEGDATPFSDV-T 973 (1141)
T ss_pred cccccchhccccccCccccceeecCCCCccccCCCcceEECcccCccccchhhhHHHhhhhhhhcccccccCCCCCcc-c
Confidence 9999999999999999999999998 35678889999999995 9
Q ss_pred HHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccc
Q psy7583 285 VQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFG 364 (451)
Q Consensus 285 ~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~G 364 (451)
+..++..|.++||+.+|+|.||||+||++|.++||+||.|||||+|||+||+|+|++||++.|||||++||+++||+|||
T Consensus 974 v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfG 1053 (1141)
T KOG0214|consen 974 VSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFG 1053 (1141)
T ss_pred hhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCeeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhCCc
Q psy7583 365 EMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444 (451)
Q Consensus 365 EME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm~I 444 (451)
|||+||++||||+++|+|||+..||.+.+++|..||.++..+.+.+.+.|+.|.+.+.++.+.+|||||||+|||+||||
T Consensus 1054 EMErdc~iahGaa~~L~ERL~~~SD~~~~~~c~~c~l~~i~~~~~n~~~ck~c~n~~~v~~v~ipya~kLl~qelmsmni 1133 (1141)
T KOG0214|consen 1054 EMERDCLIAHGAAAFLKERLFEKSDAYRVHICVLCGLTAIAGLIPNSFECRGCENKTLVVRVYIPYAAKLLFQELMSMNI 1133 (1141)
T ss_pred hhHHHHHHHhhHHHHHHHHhhccCccceEEEeccchhhhhhccCCCccccccccCccceEEEechhHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999977777777788899999999999999999999999999999999
Q ss_pred ccEEEEC
Q psy7583 445 APRLMVV 451 (451)
Q Consensus 445 ~~r~~~~ 451 (451)
.||++++
T Consensus 1134 ~pr~~~~ 1140 (1141)
T KOG0214|consen 1134 APRRKTK 1140 (1141)
T ss_pred ccccccC
Confidence 9999874
No 8
>KOG0216|consensus
Probab=100.00 E-value=2.3e-107 Score=862.76 Aligned_cols=381 Identities=38% Similarity=0.630 Sum_probs=344.4
Q ss_pred CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL 80 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~ 80 (451)
||+|++||+.|.|+++|+|++||.|+|+++.|+.+++|++|.|+||||||
T Consensus 680 mg~p~~a~~~radnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAV------------------------------ 729 (1111)
T KOG0216|consen 680 MGTPGHALRTRADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAV------------------------------ 729 (1111)
T ss_pred cCCccccchhcccCceEEecCCCCceeecccccccccccCCCCcceEEEE------------------------------
Confidence 89999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeec-CCcccccCCchhhhh
Q psy7583 81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEK-PNRQTCQGMRNAIYD 159 (451)
Q Consensus 81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~-P~~~~~~~~~~~~~~ 159 (451)
+|||||||||||||||+|+||||+++++||+.++++.+.... ...|.. |.. ...+
T Consensus 730 ---------------isyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~r-~~~F~~~p~~--------~~~~ 785 (1111)
T KOG0216|consen 730 ---------------ISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRSR-SKHFGRSPGE--------PELK 785 (1111)
T ss_pred ---------------EeecccChhhhhhhchhhhhccccceeEEeeeeechhhcccc-eeeeeeCCCC--------cccc
Confidence 999999999999999999999999999999999887654332 234553 432 2378
Q ss_pred ccCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccccccccceeeEEecCCcceEEEEEEEEeccCCe--eEEEEEEe
Q psy7583 160 KLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGY--KFCKIRVR 237 (451)
Q Consensus 160 ~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~--~~vkv~ir 237 (451)
+||.||||.||++++.||+++.-.. . + ++ +..-.+++..|+|+||.|.+..++.|. +.+.|++|
T Consensus 786 ~ld~dgLP~~G~kl~~~dp~~~y~d---~--~--t~-------~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~R 851 (1111)
T KOG0216|consen 786 KLDADGLPSIGQKLEYGDPYYAYFD---E--E--TG-------KTRIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLR 851 (1111)
T ss_pred ccCCCCCCCCcccccCCCcEEEEEc---c--c--CC-------ceEEEEecCCCCeeeEEEEEccccCCCccceEEEEEE
Confidence 9999999999999999999986432 1 0 11 223467889999999999999887776 77999999
Q ss_pred ecCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCC
Q psy7583 238 SVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFND 281 (451)
Q Consensus 238 ~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~ 281 (451)
.+|+|.||||||||||||||||+.||.+ +||++|..+|+|||..
T Consensus 852 i~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFtesGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~~Datpf~~ 931 (1111)
T KOG0216|consen 852 IPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFTESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNAQDATPFIF 931 (1111)
T ss_pred ecCCCcccchhhhhccccccccccCCCCCCCccccCcCcceeeCCCCCcccccHHHHHHHHhchhhccccccccCCceee
Confidence 9999999999999999999999999998 5789999999999863
Q ss_pred c---ccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCccccc
Q psy7583 282 A---VNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARD 358 (451)
Q Consensus 282 ~---~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~ 358 (451)
. ..++.++++|+++|||++|+|.||+|.+|++|+++||+|+||||||+|||.||+|+|++||++.+|+||++||+++
T Consensus 932 ~E~~t~~dyfg~~L~~~GyNyyGnE~~YSGv~G~e~~adIf~GvVyYQRLrHMv~DKfQVRstG~v~~~T~QPvkGRkr~ 1011 (1111)
T KOG0216|consen 932 SEENTAIDYFGEMLKKAGYNYYGNEPMYSGVDGREMRADIFFGVVYYQRLRHMVSDKFQVRSTGPVDSLTHQPVKGRKRG 1011 (1111)
T ss_pred cCcccHHHHHHHHHHHcCcCccCCcccccccccceeeeeEEEeehhHHHHHHHhcceeeeeeccCccccccCCccCcccC
Confidence 2 4679999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEee--------cccceeEeccCCCCCccceecCch
Q psy7583 359 GGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIAN--------MRNNTFECKGCKNKTQISQVRLPY 430 (451)
Q Consensus 359 Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~--------~~~~~~~C~~C~~~~~~~~v~iPy 430 (451)
||+||||||||||++|||+++|++||+.+||...++||..||+++... .......|+.|+ +..+..|+|||
T Consensus 1012 GGiRfGEMERDali~HGtsfllqDRL~~~SD~~~a~vC~~cgsil~~~~~l~~~~~~~~~~~~C~~c~-~~~~~~v~~P~ 1090 (1111)
T KOG0216|consen 1012 GGIRFGEMERDALIAHGTSFLLQDRLLNSSDYTVAEVCRTCGSILSTQQKLIKEPGGSTSTVTCRSCD-GKGVTTVAMPY 1090 (1111)
T ss_pred CCccccchhhhhHhhcchHhhhhhhhccCcchhHHHHHHHhhhhhhhhhhhhcccCCCCCceeEEecC-CCceEEEEccH
Confidence 999999999999999999999999999999999999999999998752 123466899996 45788999999
Q ss_pred hHHHHHHHHHhCCcccEEEE
Q psy7583 431 AAKLLFQELMSMNIAPRLMV 450 (451)
Q Consensus 431 ~~klL~~EL~sm~I~~r~~~ 450 (451)
+||||..||.||||++++.+
T Consensus 1091 vfkYL~aEL~amnIk~~l~l 1110 (1111)
T KOG0216|consen 1091 VFKYLTAELAAMNIKMRLDL 1110 (1111)
T ss_pred HHHHHHHHHhhCceeEEecc
Confidence 99999999999999999865
No 9
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=2.2e-103 Score=891.80 Aligned_cols=374 Identities=30% Similarity=0.439 Sum_probs=316.8
Q ss_pred ccceEe-ccCCCccceeccc----cccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccccccccCC
Q psy7583 13 DTLAHV-LYYPHKPLVTTRS----MEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPA 87 (451)
Q Consensus 13 D~~~~~-L~yPQ~Plv~T~~----~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~~el~~ 87 (451)
|+..++ +.|||+|||+|+. .+++ |++..+.++|+++
T Consensus 675 ~~~sn~~~~~~q~Plv~~~~~v~~g~~l---------------------------------------ad~~~~~~~e~~~ 715 (1112)
T PRK00405 675 FQRSNQNTCINQRPIVKVGDRVEKGDVL---------------------------------------ADGPSTDNGELAL 715 (1112)
T ss_pred cccccccceeecceeeecCCeEeeccEe---------------------------------------ecccccCcccccC
Confidence 777777 8889999988873 4443 3444445555555
Q ss_pred CcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceee-ecCCcccccCCchhhhhccCcCCC
Q psy7583 88 GINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQF-EKPNRQTCQGMRNAIYDKLDDDGI 166 (451)
Q Consensus 88 G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f-~~P~~~~~~~~~~~~~~~LD~dGi 166 (451)
|+|++||||||+||||||||||||+|+|||+|+|+||++|+.++++++.+.++.+ ..|.. ....|++||+|||
T Consensus 716 G~N~~VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~~~~~~~~~~p~~------~~~~~~~Ld~dGi 789 (1112)
T PRK00405 716 GQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNV------SEEALRNLDESGI 789 (1112)
T ss_pred CcceEEEEEeecccCccceEEEEhhhhccCceEEEEEeeeeeEeeccCCCceeecccCCCC------ChHHhhccCCCCC
Confidence 5555555599999999999999999999999999999999999887666654322 24432 2457999999999
Q ss_pred cccCcEEeCCCEEEEEeeecCCCCccccc-------cccccccceeeEEecCCcceEEEEEEEEec-cCC-------eeE
Q psy7583 167 IAPGLRVSGDDVVIGKTITLPENEDELEG-------TTKRFSKRDGSTFLRNSETGIVDQVMLTLN-VDG-------YKF 231 (451)
Q Consensus 167 ~~vG~~v~~gDiligK~~~~~~~~~~~~~-------~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~-~~g-------~~~ 231 (451)
|+||++|++|||||||++|........+. ..+....+|+|++++++|+|+||+|.++.+ .++ .+.
T Consensus 790 ~~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~ 869 (1112)
T PRK00405 790 VRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKL 869 (1112)
T ss_pred ccCccEecCCCEEEEEecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceE
Confidence 99999999999999999885422110000 011124789999999999999999999877 555 468
Q ss_pred EEEEEeecCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCcee
Q psy7583 232 CKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGD 275 (451)
Q Consensus 232 vkv~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d 275 (451)
++|++|+.|+|+||||||||||||||||+||||| +|++.|.+ |
T Consensus 870 vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~-~ 948 (1112)
T PRK00405 870 VKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK-F 948 (1112)
T ss_pred EEEEEeeecccCcccchhhccCCceeEEeEeccCCCCcCCCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCe-E
Confidence 9999999999999999999999999999999999 46777877 7
Q ss_pred ecC-CCCcccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCc
Q psy7583 276 ATP-FNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEG 354 (451)
Q Consensus 276 ~tp-F~~~~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~G 354 (451)
+|| |.+. +.+++.+.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++|
T Consensus 949 ~tp~f~~~-~~~~~~~~l~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~haRs~Gp~~~lT~QP~~G 1027 (1112)
T PRK00405 949 ATPVFDGA-KEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027 (1112)
T ss_pred ecCccCCc-cHHHHHHHHHHcCcCCCCCEEEECCCCCCCCcccEEEEehhheechhhhcchhhhcccCCccceeeCCCcc
Confidence 999 7765 89999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCccccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHH
Q psy7583 355 RARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKL 434 (451)
Q Consensus 355 r~~~Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~kl 434 (451)
|+++|||||||||+|||+||||+++|+|||+.+||++. |... .+.| .| ++..+..+.+||||||
T Consensus 1028 rsr~GG~R~GEME~d~l~a~Gas~~L~Erl~~~SD~~~-------g~~~-------~~~~-~~-~~~~i~~~~~p~~fkl 1091 (1112)
T PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVV-------GRTK-------VYEA-IV-KGENIPEPGIPESFNV 1091 (1112)
T ss_pred cccCCCeeeeeeehhhHhhhhhHHHHHHHhhccCcccc-------ccee-------EEEE-ee-cCCcccccCCChHHHH
Confidence 99999999999999999999999999999999999985 3221 3446 46 4668999999999999
Q ss_pred HHHHHHhCCcccEEE
Q psy7583 435 LFQELMSMNIAPRLM 449 (451)
Q Consensus 435 L~~EL~sm~I~~r~~ 449 (451)
|+|||+||||++++.
T Consensus 1092 L~~EL~sm~i~~~~~ 1106 (1112)
T PRK00405 1092 LVKELQSLGLDVELL 1106 (1112)
T ss_pred HHHHHHHCccceEEe
Confidence 999999999999985
No 10
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=3.3e-103 Score=886.47 Aligned_cols=347 Identities=30% Similarity=0.440 Sum_probs=296.5
Q ss_pred eccccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeee--cCCcccccCCc
Q psy7583 77 MEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFE--KPNRQTCQGMR 154 (451)
Q Consensus 77 ~~~~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~--~P~~~~~~~~~ 154 (451)
+..+.++|+++|+|++||||||+||||||||||||+|+|||+|||+||++|++++++.+.+.+ .|. .|+. +
T Consensus 663 ~~~~~~~e~~~G~N~~VAvm~y~GYn~EDAiiink~~i~rg~~~s~~~~~~~~~~~~~~~g~e-~~~~~~p~~------~ 735 (1065)
T TIGR02013 663 GPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPE-EITRDIPNV------S 735 (1065)
T ss_pred cccccCCcCcCccceEEEEEeeecccccceEEeehhhhcCCceEEEEEEEEEEEeeccCCCce-EeeccCCCC------c
Confidence 333444555555555555599999999999999999999999999999999999877665553 443 3542 2
Q ss_pred hhhhhccCcCCCcccCcEEeCCCEEEEEeeecCCCCccc--------cccccccccceeeEEecCCcceEEEEEEEEecc
Q psy7583 155 NAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL--------EGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNV 226 (451)
Q Consensus 155 ~~~~~~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~--------~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~ 226 (451)
...|++||+||||+||++|++|||||||++|........ .+. +....+|+|++++++|+|+||+|.++.+.
T Consensus 736 ~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l~~~~~~~-~~~~~~d~s~~~~~~~~g~V~~V~~~~~~ 814 (1065)
T TIGR02013 736 EEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGE-KARDVRDTSLRVPPGVEGTVIDVKVFSRK 814 (1065)
T ss_pred hhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhhhhhhccc-CCccccccceEccCCCCEEEEEEEEEecc
Confidence 457999999999999999999999999999854221100 011 11236899999999999999999998877
Q ss_pred CC-------eeEEEEEEeecCCCccccccccccCCccEEeeeehhh----------------------------------
Q psy7583 227 DG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE---------------------------------- 265 (451)
Q Consensus 227 ~g-------~~~vkv~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e---------------------------------- 265 (451)
++ ++.++|++|+.|+|+||||||||||||||||+|||||
T Consensus 815 ~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~~eDMPf~~~G~~pDiIiNPhg~PSRMtiGqllE~~~ 894 (1065)
T TIGR02013 815 QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHL 894 (1065)
T ss_pred CCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEecCCCCCccCCCCCccEEECCCCCcccccHHHHHHHHH
Confidence 66 5789999999999999999999999999999999999
Q ss_pred --Hhhhc--CCceeecC-CCCcccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeee
Q psy7583 266 --VSSNK--GEIGDATP-FNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRA 340 (451)
Q Consensus 266 --~~~~~--G~~~d~tp-F~~~~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~ 340 (451)
+|++. |.+.++|| |.+. +.+++.+.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||+
T Consensus 895 gka~~~~~~~~~~~~tp~f~~~-~~~~~~~~l~~~g~~~~G~e~l~~G~TG~~~~~~ifvG~~yy~rL~HmV~DK~haRs 973 (1065)
T TIGR02013 895 GWAGKRLGRKGVPIATPVFDGA-SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARS 973 (1065)
T ss_pred HHHHHhccCCCeEEeccCcCCc-cHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccEEEeehheeechhhhcchhhhcc
Confidence 35555 67788999 7665 899999999999999999999999999999999999999999999999999999999
Q ss_pred ccCeeeeeecCCCcccccCccccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCC
Q psy7583 341 RGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 341 ~G~~~~lt~Qp~~Gr~~~Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
+||++.|||||++||+++|||||||||+|||+||||+++|+|||+.+||++. |.. .. .+..| ++
T Consensus 974 ~Gp~~~lT~QP~~Grsr~GG~R~GEME~d~l~a~Gas~~L~E~l~~~SD~~~-------g~~-------~~-~~~~~-~~ 1037 (1065)
T TIGR02013 974 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVV-------GRT-------KA-YEAIV-KG 1037 (1065)
T ss_pred cCCccceeeCCCcccccCCCeeeeeeeHHHHHhhhhHHHHHHHHhccChhhh-------hhh-------hh-hhhhc-CC
Confidence 9999999999999999999999999999999999999999999999999994 321 11 12445 46
Q ss_pred CccceecCchhHHHHHHHHHhCCcccEE
Q psy7583 421 TQISQVRLPYAAKLLFQELMSMNIAPRL 448 (451)
Q Consensus 421 ~~~~~v~iPy~~klL~~EL~sm~I~~r~ 448 (451)
..+..+.+|||||||+|||+||||++++
T Consensus 1038 ~~i~~~~~p~sfklL~~EL~sm~i~~~~ 1065 (1065)
T TIGR02013 1038 ENVPEPGIPESFNVLIKELQSLGLDIEL 1065 (1065)
T ss_pred CccccccCCccHHHHHHHHHhCCccccC
Confidence 6899999999999999999999999975
No 11
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=7.1e-102 Score=869.35 Aligned_cols=408 Identities=29% Similarity=0.400 Sum_probs=339.4
Q ss_pred ccceEeccCCCccceeccccccccCCCCCCcceeeee----e------------------eee-----------cccCCC
Q psy7583 13 DTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVA----I------------------LCY-----------TGYNQE 59 (451)
Q Consensus 13 D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVA----V------------------~sy-----------tgynqe 59 (451)
-..+..|.+|++|+|.|-.-.....| +|. +|+| + ..| ||+||+
T Consensus 543 qrQaVPll~~e~p~VgTg~e~~~a~d---s~~-~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rsNq~t~i~qr 618 (1077)
T CHL00207 543 QRQAVPLLYPEKPIVGTGYEKQIALD---SGM-TIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYR 618 (1077)
T ss_pred ccccccccccCCCeEECCcchHhhhh---cch-heEeccCcEEEEecCcEEEEEeCCCceeEEEeccccccccCceeecc
Confidence 34678899999999999443333333 222 2222 0 012 555556
Q ss_pred CcEEeccceeccceEeeeccccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcc
Q psy7583 60 DSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQE 139 (451)
Q Consensus 60 d~~~~n~~~i~rG~~r~~~~~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~ 139 (451)
+.++.+.+.-+.-.+|+++++.++|+++|+|++||||||+||||||||||||++++||+|||+|+++|+.++++++.+.+
T Consensus 619 p~V~~G~~v~~G~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~g~e 698 (1077)
T CHL00207 619 PIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSE 698 (1077)
T ss_pred cccCCCCEEecCCEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCCCce
Confidence 66665554333337999999999999999999999999999999999999999999999999999999999887766654
Q ss_pred eeee--cCCcccccCCchhhhhccCcCCCcccCcEEeCCCEEEEEeeecCCCCcc----c----cccccccccceeeEEe
Q psy7583 140 EQFE--KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDE----L----EGTTKRFSKRDGSTFL 209 (451)
Q Consensus 140 ~~f~--~P~~~~~~~~~~~~~~~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~----~----~~~~~~~~~~d~s~~~ 209 (451)
.|+ .|+. ....|++||+||||+||++|++|||||||++|..+.... + .++ +....+|+|+++
T Consensus 699 -~i~~~~p~~------~~~~~~~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~-~~~~~kd~sl~~ 770 (1077)
T CHL00207 699 -EITRNIPNV------SEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGE-KAKDVKDTSLRM 770 (1077)
T ss_pred -EEeccCCCC------ChHHhhccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhcc-CCCcceEeEEEc
Confidence 344 4543 245799999999999999999999999999985322110 0 111 123578999999
Q ss_pred cCCcceEEEEEEEEecc--CCe-----eEEEEEEeecCCCccccccccccCCccEEeeeehhh-----------------
Q psy7583 210 RNSETGIVDQVMLTLNV--DGY-----KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE----------------- 265 (451)
Q Consensus 210 ~~~e~g~Vd~V~i~~~~--~g~-----~~vkv~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e----------------- 265 (451)
+++++|+||+|.++.+. ++. ..+||++|+.|+|+||||||||||||||||+|||+|
T Consensus 771 ~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~~dG~~pDiIlNP 850 (1077)
T CHL00207 771 PNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNP 850 (1077)
T ss_pred CCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCccCCCCCccEEECC
Confidence 99999999999998753 332 358999999999999999999999999999999999
Q ss_pred -------------------HhhhcCCceeecCCCCcccHHHHHHHHHHh---------------CCCCCCcEEEEcCccC
Q psy7583 266 -------------------VSSNKGEIGDATPFNDAVNVQKISTLLQEY---------------GYQLRGNEVMFNGHTG 311 (451)
Q Consensus 266 -------------------~~~~~G~~~d~tpF~~~~~~~~~~~~l~~~---------------g~~~~g~~~~~~g~tG 311 (451)
+|++.|...++|||++. ..+++++.|.+. +|+++|++.||||+||
T Consensus 851 hg~PSRMtiGqllE~~lGka~~~l~~~~~~tpF~~~-~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~Gk~~lydG~TG 929 (1077)
T CHL00207 851 LGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEM-YGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTG 929 (1077)
T ss_pred ccccccccHHHHHHHHHHHHHHhcCCcEeeccCCCC-cHHHHHHHHHhhhhhhccchhccccccCCCCCCCEEEECCCCC
Confidence 45666777889999986 677777766553 3788999999999999
Q ss_pred ceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccchhhHHHHHhcchhHHHHHhhcccCCce
Q psy7583 312 RKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPY 391 (451)
Q Consensus 312 ~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~ 391 (451)
++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++|||||||||+|||+|||||++|+|||+.+||++
T Consensus 930 e~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~s~lTqQP~~Grsr~GG~RfGEME~~aL~a~GAa~~L~E~L~~kSD~~ 1009 (1077)
T CHL00207 930 YKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDM 1009 (1077)
T ss_pred CCccCceEEEecceeEchhhccccceeeccCCCcccccCCCCccccCCCeeeecccHHHHHhhhhHHHHHHHhhcCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhCCcccEEE
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 449 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm~I~~r~~ 449 (451)
.++ ...|..|.++.++.++.+|||||+|+|||+||||++.+.
T Consensus 1010 ~~r----------------~~~~~~~~~~~~i~~~~~P~sfklL~~EL~sl~i~~~~~ 1051 (1077)
T CHL00207 1010 QGR----------------NETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAY 1051 (1077)
T ss_pred eeh----------------HHHHHhhhCCCeecCCCCCchHHHHHHHHHHCCcCcEec
Confidence 742 123888988889999999999999999999999999875
No 12
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=4.2e-100 Score=858.26 Aligned_cols=372 Identities=27% Similarity=0.364 Sum_probs=317.4
Q ss_pred cccCCCCcEEeccceeccc-eEeeeccccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeec
Q psy7583 54 TGYNQEDSVILNASAVERG-YFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAES 132 (451)
Q Consensus 54 tgynqed~~~~n~~~i~rG-~~r~~~~~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~ 132 (451)
||++|.|.++.+ -.++-| ..|+++++.+||+++|+|++||||||+||||||||||||+|++||+|||+||++|+.+++
T Consensus 618 t~~~QkPlV~~g-~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~ 696 (1070)
T CHL00001 618 TCMHQKPQVRRG-KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTH 696 (1070)
T ss_pred cccccCCEEecC-CEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEe
Confidence 555667777766 345555 789999999999999999999999999999999999999999999999999999999988
Q ss_pred ccCCCcceeee--cCCcccccCCchhhhhccCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccc---------cccc
Q psy7583 133 KRIGDQEEQFE--KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTT---------KRFS 201 (451)
Q Consensus 133 ~~~~~~~~~f~--~P~~~~~~~~~~~~~~~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~---------~~~~ 201 (451)
+++.+. |.++ .|+.+ ...|++||+|||++||++|++|||||||++|....+....++. +...
T Consensus 697 ~~~~g~-e~i~~~~p~~~------~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~ 769 (1070)
T CHL00001 697 VTSQGP-ERITKEIPHLE------AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVST 769 (1070)
T ss_pred ccCCCc-ceEeccCCCCc------hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCc
Confidence 776665 4444 35432 3579999999999999999999999999998632221111111 1235
Q ss_pred cceeeEEecCCcceEEEEEEEEe----ccCCeeEEEEEEeecCCCccccccccccCCccEEeeeehhh------------
Q psy7583 202 KRDGSTFLRNSETGIVDQVMLTL----NVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE------------ 265 (451)
Q Consensus 202 ~~d~s~~~~~~e~g~Vd~V~i~~----~~~g~~~vkv~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------ 265 (451)
.+|+|++++++++|+|++|.++. +.++.+.|||++|+.|+|+||||||||||||||||+|||+|
T Consensus 770 ~~d~sl~~~~~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~~dG~~pD 849 (1070)
T CHL00001 770 SKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVD 849 (1070)
T ss_pred ceeCeEECCCCCceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcccCCCCCc
Confidence 78999999999999999999887 35567899999999999999999999999999999999999
Q ss_pred ------------------------HhhhcCCceeecCCCCcccHHHHH-----HHHHHhCC----------CCCCcEEEE
Q psy7583 266 ------------------------VSSNKGEIGDATPFNDAVNVQKIS-----TLLQEYGY----------QLRGNEVMF 306 (451)
Q Consensus 266 ------------------------~~~~~G~~~d~tpF~~~~~~~~~~-----~~l~~~g~----------~~~g~~~~~ 306 (451)
+|++.|.+.|+|||++. ..++++ +.|.++|+ +++|++.||
T Consensus 850 iIlNP~gvPSRMtiGqllE~~~G~a~~~~g~~~~~~pf~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~Gk~~l~ 928 (1070)
T CHL00001 850 MVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDER-YEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLF 928 (1070)
T ss_pred eeeccccccccccHHHHHHHHhHHHHhhcCceeeeccCCCc-chhhhhhhhhhHHHHHHHHhcCCceeccCCCCCeEEEE
Confidence 46778999999999976 555555 56777776 455999999
Q ss_pred cCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccchhhHHHHHhcchhHHHHHhhcc
Q psy7583 307 NGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFE 386 (451)
Q Consensus 307 ~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~GEME~~~l~~~g~~~~l~e~l~~ 386 (451)
||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++|||||||||+|||+|||||++|+|||+.
T Consensus 929 dG~TG~~~~~~i~vG~~Yy~kL~HmV~DKihaRs~Gp~~~lT~QP~~Grsr~GG~RfGEME~~al~a~GAs~~L~E~L~~ 1008 (1070)
T CHL00001 929 DGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTY 1008 (1070)
T ss_pred cCCCCCCccceEEEEecceeEchhhccccceeeccCCCcccccCCCCcccCCCCeeeecchHHHHHhhhHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCceeeeeeccccceEEeecccceeEeccCCCCCccce-ecCchhHHHHHHHHHhCCcccEEEE
Q psy7583 387 VSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQ-VRLPYAAKLLFQELMSMNIAPRLMV 450 (451)
Q Consensus 387 ~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~-v~iPy~~klL~~EL~sm~I~~r~~~ 450 (451)
+||+...+ |. .+.|..+ +..+.+ +.+|||||+|++||+|||+++.+..
T Consensus 1009 ~SD~~~~r-~~-------------~~~~i~~--g~~~~~~~~~pesfk~l~~El~~l~l~i~~~~ 1057 (1070)
T CHL00001 1009 KSDHIRAR-QE-------------VLGAIIT--GGTIPKPEDAPESFRLLVRELRSLALELNHFL 1057 (1070)
T ss_pred cCccHHHH-HH-------------HHHhhhc--CCcccCCCCCCchhhHHHHHHHhCccceEEEE
Confidence 99998764 21 1222223 335666 7999999999999999999998864
No 13
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=3e-93 Score=829.35 Aligned_cols=371 Identities=28% Similarity=0.375 Sum_probs=324.6
Q ss_pred cccCCCCcEEeccceeccc-eEeeeccccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeec
Q psy7583 54 TGYNQEDSVILNASAVERG-YFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAES 132 (451)
Q Consensus 54 tgynqed~~~~n~~~i~rG-~~r~~~~~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~ 132 (451)
||+||+|.+..+.. ++.| ..+++++++.|||++|+|++||||+|.|||+||||+||++.+.+++|||+|+..|+.+.+
T Consensus 773 TcinqrPiV~~Gd~-V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD~fTSIHIee~ei~~r 851 (2890)
T PRK09603 773 TSFNQVPIVKVGDK-VEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDAR 851 (2890)
T ss_pred ceeeeccEecCCCE-eccCCEEecCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCccceEEEEeeeEEEEE
Confidence 55666666666554 3444 799999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcce-eeecCCcccccCCchhhhhccCcCCCcccCcEEeCCCEEEEEeeecCCCCcccccc---------cccccc
Q psy7583 133 KRIGDQEE-QFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGT---------TKRFSK 202 (451)
Q Consensus 133 ~~~~~~~~-~f~~P~~~~~~~~~~~~~~~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~---------~~~~~~ 202 (451)
.++.+.|+ +..+|+- .+...++||++||+++|++|++|||||||++|..+.. +.++ ++....
T Consensus 852 ~Tk~G~EeITrdIPnv------se~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~--~tPEekLLraIFGeka~~v 923 (2890)
T PRK09603 852 ELKHGVEEFTADIPDV------KEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIK--STPEERLLRAIFGDKAGHV 923 (2890)
T ss_pred ecCCCCcEEeccCCCC------CHHHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCC--CChHHHHHHHHhccccccc
Confidence 88888765 4567754 3678899999999999999999999999999975322 2222 245578
Q ss_pred ceeeEEecCCcceEEEEEEEEecc--------------------------------------------------------
Q psy7583 203 RDGSTFLRNSETGIVDQVMLTLNV-------------------------------------------------------- 226 (451)
Q Consensus 203 ~d~s~~~~~~e~g~Vd~V~i~~~~-------------------------------------------------------- 226 (451)
+|+|++++++..|+|.+|.+....
T Consensus 924 kDtSLrvp~G~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1003 (2890)
T PRK09603 924 VNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGK 1003 (2890)
T ss_pred ccCceecCCCCcEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhccccccccccccccc
Confidence 999999999999999999876521
Q ss_pred --------------------------------------------------------------CC-------eeEEEEEEe
Q psy7583 227 --------------------------------------------------------------DG-------YKFCKIRVR 237 (451)
Q Consensus 227 --------------------------------------------------------------~g-------~~~vkv~ir 237 (451)
+| .+.|||+||
T Consensus 1004 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~Gv~~~VkV~ia 1083 (2890)
T PRK09603 1004 DYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIA 1083 (2890)
T ss_pred cccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCCCcceEEEEEEE
Confidence 01 357999999
Q ss_pred ecCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCc--------
Q psy7583 238 SVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEI-------- 273 (451)
Q Consensus 238 ~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~-------- 273 (451)
+.|+|+||||||||||||||||+|||+| +|+..|.+
T Consensus 1084 ~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~lg~~i~~~~~~~ 1163 (2890)
T PRK09603 1084 TKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDK 1163 (2890)
T ss_pred EeecccccchhhhccCCCeeEEEEEchhcCCCCCCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHhcCcChhhhhhhc
Confidence 9999999999999999999999999999 23444432
Q ss_pred -------------------------------------------------eeecC-CCCcccHHHHHHHHHHhCCCCCCcE
Q psy7583 274 -------------------------------------------------GDATP-FNDAVNVQKISTLLQEYGYQLRGNE 303 (451)
Q Consensus 274 -------------------------------------------------~d~tp-F~~~~~~~~~~~~l~~~g~~~~g~~ 303 (451)
.++|| |++. +.+++.+.|.++||+.+|++
T Consensus 1164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~tpvF~g~-~~~~i~~~l~~aG~~~~Gk~ 1242 (2890)
T PRK09603 1164 TKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGI-SQEKFYKLFELAKIAMDGKM 1242 (2890)
T ss_pred chhhhHHHHHHHHhhhcccccccccccccccccchHHHHhhhhhhccCCcccCCCCCCC-CHHHHHHHHHHcCCCCCCCE
Confidence 35788 8776 89999999999999999999
Q ss_pred EEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccchhhHHHHHhcchhHHHHHh
Q psy7583 304 VMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRER 383 (451)
Q Consensus 304 ~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~GEME~~~l~~~g~~~~l~e~ 383 (451)
.||||+|||+|+++||+|++|||||+|||+||+|||++|||+.|||||++||+++|||||||||+|||+||||+++|+||
T Consensus 1243 ~LyDGrTGe~f~~~V~vG~~YylKL~HmVdDKiHaRstGPyslvTqQPl~GKs~~GGqRfGEMEvwALeAyGAa~~LqE~ 1322 (2890)
T PRK09603 1243 DLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEM 1322 (2890)
T ss_pred EEEcCCCCCCccceEEEEeeceeechhhccchhhhccCCCcchhhhCCCcccccCCCceeeeeeHHHHHHhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhCCcccEEEE
Q psy7583 384 LFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMV 450 (451)
Q Consensus 384 l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm~I~~r~~~ 450 (451)
|+.+||++..+. ..|..|.++.++..+.+|||||+|++||+||||++++..
T Consensus 1323 Lt~kSDdv~gR~----------------~~y~~i~~g~~i~~~~iPeSFkvL~~EL~sL~l~i~~~~ 1373 (2890)
T PRK09603 1323 LTIKSDDIRGRE----------------NAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFG 1373 (2890)
T ss_pred HhcCCcchhhhh----------------hhhhhhcCCCcccccCCCHHHHHHHHHHHhCCcceEEEe
Confidence 999999997431 135667777889999999999999999999999999863
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=8.9e-88 Score=781.25 Aligned_cols=372 Identities=29% Similarity=0.401 Sum_probs=315.0
Q ss_pred cccCCCCcEEeccceeccceEeeeccccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecc
Q psy7583 54 TGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESK 133 (451)
Q Consensus 54 tgynqed~~~~n~~~i~rG~~r~~~~~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~ 133 (451)
||+||.|.+..+..-.+.-..|++++++.|||++|+|++||||+|.|||+||||+||++.+.+++|||+|+..|+++.+.
T Consensus 783 TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliSErlv~eD~fTSiHIee~ei~~r~ 862 (2836)
T PRK14844 783 TCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHD 862 (2836)
T ss_pred eeeeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccCCcccccccccchhhccCceeEEEeecceEEEEEe
Confidence 55555665555554333336999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCCcce-eeecCCcccccCCchhhhhccCcCCCcccCcEEeCCCEEEEEeeecCCCCcccccc---------ccccccc
Q psy7583 134 RIGDQEE-QFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGT---------TKRFSKR 203 (451)
Q Consensus 134 ~~~~~~~-~f~~P~~~~~~~~~~~~~~~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~---------~~~~~~~ 203 (451)
++.+.|+ +..+|+. .+...++||++||+++|++|++|||||||++|..+.. +.++ ++....+
T Consensus 863 Tk~G~EeITrdIPnv------~e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~--~tPEekLL~aIFGek~~~vk 934 (2836)
T PRK14844 863 TPLGSEKITRAIPGV------NEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLS--LPPETKLLMTIFGEKSFDCA 934 (2836)
T ss_pred ccCCCceecccCCCC------ChHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCC--CCHHHHHHHHHhCCcccccc
Confidence 8888765 3556754 3678899999999999999999999999999875432 2222 2556789
Q ss_pred eeeEEecCCcceEEEEEEEEecc---------------------------------------------------------
Q psy7583 204 DGSTFLRNSETGIVDQVMLTLNV--------------------------------------------------------- 226 (451)
Q Consensus 204 d~s~~~~~~e~g~Vd~V~i~~~~--------------------------------------------------------- 226 (451)
|+|++++++..|+|.+|.+....
T Consensus 935 dtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1014 (2836)
T PRK14844 935 DSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQDREKFDSIE 1014 (2836)
T ss_pred cCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhcccccccHHHHhhcc
Confidence 99999999999999999877532
Q ss_pred --------------------------------------------CC-------eeEEEEEEeecCCCccccccccccCCc
Q psy7583 227 --------------------------------------------DG-------YKFCKIRVRSVRIPQIGDKFASRHGQK 255 (451)
Q Consensus 227 --------------------------------------------~g-------~~~vkv~ir~~R~p~IGDKFsSRHGQK 255 (451)
+| .+.|||+|.+.|.+++|||+|+|||||
T Consensus 1015 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyia~KRkiqvGDKmAGRHGNK 1094 (2836)
T PRK14844 1015 REQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNK 1094 (2836)
T ss_pred HHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEEEEeecCCccccccccCCCC
Confidence 11 357999999999999999999999999
Q ss_pred cEEeeeehhh------------------------------------HhhhcCC---------------------------
Q psy7583 256 GTCGIQYRQE------------------------------------VSSNKGE--------------------------- 272 (451)
Q Consensus 256 Gvvs~i~~~e------------------------------------~~~~~G~--------------------------- 272 (451)
||||.|+|.| +|...|.
T Consensus 1095 GVIS~IlP~eDMPyL~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1174 (2836)
T PRK14844 1095 GVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEINKIKSAFCKGIRSLNDDN 1174 (2836)
T ss_pred ceEeEEcccCCCCcCCCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhhHhhhhhhhccccccccccccccccc
Confidence 9999999998 1111110
Q ss_pred --------------------------------------------------------------------------------
Q psy7583 273 -------------------------------------------------------------------------------- 272 (451)
Q Consensus 273 -------------------------------------------------------------------------------- 272 (451)
T Consensus 1175 ~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1254 (2836)
T PRK14844 1175 FTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDI 1254 (2836)
T ss_pred cccccccccccccccccccccccccccccccccccccccccchhccccccchhhHHHHHHHHHhhhcccccccccccccc
Confidence
Q ss_pred ---------------ceeecC-CCCcccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCcee
Q psy7583 273 ---------------IGDATP-FNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKI 336 (451)
Q Consensus 273 ---------------~~d~tp-F~~~~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~ 336 (451)
+.-+|| |+.. +.+++.+.|+++||+.+|++.||||+||++|+++||+|++|||||+|||+||+
T Consensus 1255 ~~~~~~~~~~~~~~g~~~~tpvf~g~-~~~~i~~~L~~~g~~~~Gk~~l~dG~TGe~f~~~v~vG~~yy~kL~HmV~DKi 1333 (2836)
T PRK14844 1255 SDNNLIEFARKLRDGIPVAAPVFEGP-KDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKI 1333 (2836)
T ss_pred cHHHHHHHHhhhccCCeecCCCcCCC-CHHHHHHHHHHhCcCCCCCEEEEcCCCCCccchhheeCcchhhhhhhhhcchh
Confidence 011455 4444 78999999999999999999999999999999999999999999999999999
Q ss_pred eeeeccCeeeeeecCCCcccccCccccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEecc
Q psy7583 337 HSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKG 416 (451)
Q Consensus 337 ~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~ 416 (451)
|+|++||++.|||||++||+++|||||||||+|||+||||+++|+|||+.+||++..++|.- |..
T Consensus 1334 haRs~Gp~s~lT~QPl~Gr~~~GG~RfGEME~~al~a~Gaa~~L~E~Lt~kSD~~~gr~~~~---------------~~i 1398 (2836)
T PRK14844 1334 HARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIY---------------ESI 1398 (2836)
T ss_pred hhcccCCCcccccCCCcccccCCCceeecchHHHHHHHhHHHHHHHHhcccccchhhhhHhh---------------hhh
Confidence 99999999999999999999999999999999999999999999999999999998554321 333
Q ss_pred CCCCCccceecCchhHHHHHHHHHhCCcccEEEE
Q psy7583 417 CKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMV 450 (451)
Q Consensus 417 C~~~~~~~~v~iPy~~klL~~EL~sm~I~~r~~~ 450 (451)
|+.. ......+|||||+|+|||+||||++++.+
T Consensus 1399 vkG~-~~~~~~~PesfkvL~~EL~sl~i~~~~~~ 1431 (2836)
T PRK14844 1399 IKGD-SNFECGIPESFNVMIKELRSLCLNVDLKQ 1431 (2836)
T ss_pred ccCC-CCCcCCCCchHHHHHHHHHhCccceEEec
Confidence 3322 33345899999999999999999999875
No 15
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 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 polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=5e-84 Score=667.53 Aligned_cols=310 Identities=46% Similarity=0.757 Sum_probs=252.3
Q ss_pred CcccccCcccCCccceEeccCCCccceecc-ccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeecc
Q psy7583 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTR-SMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEY 79 (451)
Q Consensus 1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~-~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~ 79 (451)
||+|.+|+..|+|+.. .|||+|||+|. .++..+ +++++..
T Consensus 29 ~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~------------------------------------ilad~~~ 69 (386)
T PF00562_consen 29 IGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQ------------------------------------ILADGPS 69 (386)
T ss_dssp CSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTT------------------------------------ECEE-TT
T ss_pred ccceeeeeeeccCcce---eccccceEEeeccccccC------------------------------------ccccccc
Confidence 6899999999999988 99999999998 777654 2344555
Q ss_pred ccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCc-ceeeecCCcccccCCchhhh
Q psy7583 80 LRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQ-EEQFEKPNRQTCQGMRNAIY 158 (451)
Q Consensus 80 ~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~-~~~f~~P~~~~~~~~~~~~~ 158 (451)
+.++|+++|+|++||||||+||||||||||||+|++||+|||+||++ +.+++.+..+. ++.+..|+.. +...|
T Consensus 70 ~~~~e~~~G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~g~~e~~~~~~~~~-----~~~~~ 143 (386)
T PF00562_consen 70 TKFGELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKGGPSEEIFRPIPNV-----KEYNY 143 (386)
T ss_dssp ECTTTS-SSEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETTSEEBBESS--TSS-----TSTTG
T ss_pred cccccCcceeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccCCcccccccccccc-----hhhhh
Confidence 66666666666666669999999999999999999999999999999 77766555555 5555554432 45789
Q ss_pred hccCcCCCcccCcEEeCCCEEEEEeeecCCC---CccccccccccccceeeEEecCCcceEEEEEEE-------EeccCC
Q psy7583 159 DKLDDDGIIAPGLRVSGDDVVIGKTITLPEN---EDELEGTTKRFSKRDGSTFLRNSETGIVDQVML-------TLNVDG 228 (451)
Q Consensus 159 ~~LD~dGi~~vG~~v~~gDiligK~~~~~~~---~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i-------~~~~~g 228 (451)
++||+||||++|++|++||+||||++..+.. ......+ +....+|+|++++.+|.|+||+|.+ ..+.++
T Consensus 144 ~~LD~dGii~~G~~v~~gDiligk~~~~~~~~~~~~~~~~~-~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~ 222 (386)
T PF00562_consen 144 SKLDEDGIIKIGSRVEKGDILIGKITSPPRFSPLLKKIFGE-KNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEG 222 (386)
T ss_dssp GGBCTTSBB-TTCEEETTSEEEEEEESTSC--HHHHHHHHS-SSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTC
T ss_pred hhcccccccccCcEEecceeEEEEEecccccccchhhcccc-ccccccceeecccccEEeEeccccccccccccccccCc
Confidence 9999999999999999999999999611110 0011111 1223689999999999999999999 678889
Q ss_pred eeEEEEEEeecCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCC
Q psy7583 229 YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGE 272 (451)
Q Consensus 229 ~~~vkv~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~ 272 (451)
...++|++|+.|+|+||||||||||||||||+|||+| ++++.|.
T Consensus 223 ~~~iki~ir~~R~p~iGDKfssRHGqKGVvs~i~~~eDMPft~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~ 302 (386)
T PF00562_consen 223 YKKIKIRIRSTRRPQIGDKFSSRHGQKGVVSKILPQEDMPFTEDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGR 302 (386)
T ss_dssp EEEEEEEEEEEEE--TTEEEEETTSEEEEEEEEE-TTTSEEETTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTC
T ss_pred ceEEEEEecccccchhHHHHhhhhcCceEEeeeeccccCccccCCCcceeeecccccccccchHHHHhhhhhhhhhcccc
Confidence 9999999999999999999999999999999999998 4678999
Q ss_pred ceeecCCCCcccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCC
Q psy7583 273 IGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPM 352 (451)
Q Consensus 273 ~~d~tpF~~~~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~ 352 (451)
+.|+|||.+. +.+++.+.|.++||+.+|+|.||||+||++++++||+|++|||||+|||+||+|||++||++.|||||+
T Consensus 303 ~~~~t~F~~~-~~~~i~~~l~~~g~~~~g~~~l~~g~tG~~~~~~i~~G~~yy~rL~Hmv~DK~h~Rs~Gp~~~lT~QP~ 381 (386)
T PF00562_consen 303 FVDATPFDES-SEEDISELLKKAGYNYPGKEVLYDGRTGEKFEAPIFIGPVYYQRLKHMVDDKIHARSRGPYSLLTRQPV 381 (386)
T ss_dssp EEB-TTTSSS--HHHHHHHHHHTTSHTTSEEEEBESSSSSBESSEEEEEEEEEEEBSTCGGGSTEEESS--BBSSSSSB-
T ss_pred ceecCCCCCc-chhhhHhhhhcccccccceEEEEcCccCceEEeEEEeeeEEeccceEeCCcEEEEEecCCCccccCCCC
Confidence 9999999987 789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Ccccc
Q psy7583 353 EGRAR 357 (451)
Q Consensus 353 ~Gr~~ 357 (451)
+||+|
T Consensus 382 ~Gr~r 386 (386)
T PF00562_consen 382 EGRSR 386 (386)
T ss_dssp SSSSS
T ss_pred CCCCC
Confidence 99986
No 16
>PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed switch 4. The switches within the polymerase are thought to signal different stages of transcription [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M 2O5I_M ....
Probab=99.97 E-value=8.7e-32 Score=220.04 Aligned_cols=81 Identities=56% Similarity=0.948 Sum_probs=76.5
Q ss_pred CccccchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHH
Q psy7583 359 GGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQE 438 (451)
Q Consensus 359 Gg~r~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~E 438 (451)
|||||||||||||++|||+++|+|||+++||.++++||.+||++++ .|+.+.++..+.+|||||||+||
T Consensus 1 GG~R~GEMErd~LiahGas~~L~erl~~~SD~~~~~vc~~cg~~~~-----------~~~~~~~~~~~~ipy~~klL~~E 69 (81)
T PF04560_consen 1 GGLRFGEMERDALIAHGASFLLKERLFDKSDKYEIDVCSRCGSIAS-----------ICKGKPEVKKIEIPYSFKLLIQE 69 (81)
T ss_dssp CBEEEEHHHHHHHHHTTBHHHHHHHHTTTTTEEEEEEECCCHHHHH-----------TTTTSSSEEEEEEEHHHHHHHHH
T ss_pred CCcchhHHHHHHHHHhhHHHHHHHHhcCCCcCcchhhhccCCCcee-----------EECCCCeEEeeeCCHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999865 56667789999999999999999
Q ss_pred HHhCCcccEEEE
Q psy7583 439 LMSMNIAPRLMV 450 (451)
Q Consensus 439 L~sm~I~~r~~~ 450 (451)
|+||||++|+.+
T Consensus 70 L~sm~I~~~~~~ 81 (81)
T PF04560_consen 70 LRSMGIKIRIKT 81 (81)
T ss_dssp HHCTTEEEEEEE
T ss_pred HHHCcCceEEeC
Confidence 999999999975
No 17
>KOG0214|consensus
Probab=98.64 E-value=2.4e-09 Score=117.60 Aligned_cols=310 Identities=15% Similarity=0.067 Sum_probs=197.9
Q ss_pred EeeeccccccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCC
Q psy7583 74 FRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGM 153 (451)
Q Consensus 74 ~r~~~~~~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~ 153 (451)
.++.++....||++|+|+ +.+.++..++...-|--..+++++|+++...|--..+.........++.+-.......
T Consensus 728 t~~~e~l~~~eL~aG~Na----iVAi~~~~GYNqEDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~~~ee~~~~~~~~~ 803 (1141)
T KOG0214|consen 728 TRAMEYLRFRELPAGQNA----IVAIACYSGYNQEDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQGPEEIFEEPPRGE 803 (1141)
T ss_pred HHHHhhhhhhhcccccce----EEEEecccCccHHHHHHHHhhhhhcchhhhhhhhHHHhhhhhcccccccccccccccc
Confidence 455677778899999997 6899999999999999999999999998876543332211111111222211111111
Q ss_pred chhhhhccCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccc-cccccceeeEEecCCcceEEEEEEEEeccCCeeEE
Q psy7583 154 RNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTT-KRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFC 232 (451)
Q Consensus 154 ~~~~~~~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~-~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~v 232 (451)
+...+ +.-.|-+- ..|=+-+|-.... .+-+.+.. ......|.+-.-..--.++.+++.+..+..| ...
T Consensus 804 ~~~mr-~~~~dkLd------ddG~i~~G~~vs~---~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G-ivd 872 (1141)
T KOG0214|consen 804 GRGMR-NGKYDKLD------DDGIIMPGSRVSG---GDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG-IVD 872 (1141)
T ss_pred ccccc-cccccccc------ccCCccccceeec---CCEEeccccCCcccchhccccccccccccceeecccCCcc-eEE
Confidence 11111 11111111 1222223321110 11111110 0000111111000011446777888777777 444
Q ss_pred EEEEeecCCCccccccccccCCccEEeeeehhhHh--hhcCCce-----eecCCC----------------CcccHHHHH
Q psy7583 233 KIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVS--SNKGEIG-----DATPFN----------------DAVNVQKIS 289 (451)
Q Consensus 233 kv~ir~~R~p~IGDKFsSRHGQKGvvs~i~~~e~~--~~~G~~~-----d~tpF~----------------~~~~~~~~~ 289 (451)
+|.++. ++.|+||+.+|.+++-+.++-...++ ..+|... ..-||. ..+++.++-
T Consensus 873 ~V~vt~---n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~~qedmpft~eGi~pDiiiNPhaiPSRmtig~li 949 (1141)
T KOG0214|consen 873 QVWVTK---NSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITYRQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLI 949 (1141)
T ss_pred EEEEec---CCCCCceeEEEEeecccccccchhccccccCccccceeecCCCCccccCCCcceEECcccCccccchhhhH
Confidence 555555 99999999999999999998776633 2233221 123343 234666666
Q ss_pred HHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccchhhHH
Q psy7583 290 TLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERD 369 (451)
Q Consensus 290 ~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~GEME~~ 369 (451)
+-|. |-..-++..++++.+... -+-.+++..+++...|+..++.+++.+++....+++++.+.-..+..++++|+..
T Consensus 950 Ec~l--gk~~a~~~e~~~atpFs~-v~v~~is~~l~~~g~~~~G~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih 1026 (1141)
T KOG0214|consen 950 ECLL--GKVAAYEGEEGDATPFSD-VTVSKISANLHVYGYQYRGNERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIH 1026 (1141)
T ss_pred HHhh--hhhhhcccccccCCCCCc-cchhcccchHHHhccccCCCEEEecCCCCceeeeeeecCchHHHHHHHhhhheee
Confidence 6553 223333445555555555 4556788999999999999999999999999999999999999999999999999
Q ss_pred HHHhcchhHHHHHhhcccCCceeeeeeccccceEE
Q psy7583 370 CQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAI 404 (451)
Q Consensus 370 ~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~ 404 (451)
+=.+++..-+.++.+...|++.-.++|.-|+..+.
T Consensus 1027 ~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~i 1061 (1141)
T KOG0214|consen 1027 SRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLI 1061 (1141)
T ss_pred ecccCCceeeeccccccccccCCeeeehhHHHHHH
Confidence 99999999999999999999999999998886543
No 18
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=98.31 E-value=2.7e-07 Score=106.23 Aligned_cols=62 Identities=27% Similarity=0.448 Sum_probs=52.4
Q ss_pred CCCccceeccc--------c--ccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccccc
Q psy7583 21 YPHKPLVTTRS--------M--EYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 21 yPQ~Plv~T~~--------~--~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
.-|||+|.--- + -...++++|+|+||+||+|||+|||+||++++|+.++++|+|++.++..+
T Consensus 615 i~qrp~V~~G~~v~~G~iladg~~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~ 686 (1077)
T CHL00207 615 INYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY 686 (1077)
T ss_pred eecccccCCCCEEecCCEEecchhccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEe
Confidence 45799996511 2 23568999999999999999999999999999999999999998776655
No 19
>CHL00001 rpoB RNA polymerase beta subunit
Probab=98.08 E-value=1.3e-06 Score=101.08 Aligned_cols=66 Identities=27% Similarity=0.461 Sum_probs=61.8
Q ss_pred ceEeccC---------CCccceecccccccc------------CCCCCCcceeeeeeeeecccCCCCcEEeccceeccce
Q psy7583 15 LAHVLYY---------PHKPLVTTRSMEYLR------------FRELPAGINSIVAILCYTGYNQEDSVILNASAVERGY 73 (451)
Q Consensus 15 ~~~~L~y---------PQ~Plv~T~~~~~~~------------~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~ 73 (451)
..|++.| ||+|||+|. ++++ +.++|+|+|++||+|||+|||+||++++|+.++++|+
T Consensus 605 ~y~l~~y~rsnq~t~~~QkPlV~~g--~~v~~g~~ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~ 682 (1070)
T CHL00001 605 SIPLVMYQRSNKNTCMHQKPQVRRG--KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDI 682 (1070)
T ss_pred EEEeeceeccCCCcccccCCEEecC--CEEccCCEeccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCc
Confidence 6789999 999999998 8887 9999999999999999999999999999999999999
Q ss_pred Eeeeccccc
Q psy7583 74 FRSMEYLRF 82 (451)
Q Consensus 74 ~r~~~~~~~ 82 (451)
+++.++-.+
T Consensus 683 ~~s~~~~~~ 691 (1070)
T CHL00001 683 YTSFHIRKY 691 (1070)
T ss_pred eEEEEEeee
Confidence 998887665
No 20
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=93.79 E-value=0.023 Score=62.83 Aligned_cols=38 Identities=32% Similarity=0.559 Sum_probs=33.1
Q ss_pred CcceeeeeeeeecccCCCCcEEeccceeccceEeeeccccc
Q psy7583 42 AGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 42 ~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
+-+-|+.+- +||||||++++|+++++||++++.++..+
T Consensus 206 N~iVAvmsy---~GYn~EDAiIiNkssidRGlf~s~~~k~~ 243 (605)
T PRK07225 206 NFVVAVMSY---EGYNIEDALIMNKASIERGLGRSHFFRTY 243 (605)
T ss_pred eEEEEEECc---CCCChhHeeeeehhhhhcCceEEEEEEEE
Confidence 345677777 99999999999999999999999888665
No 21
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=92.95 E-value=0.038 Score=61.13 Aligned_cols=38 Identities=32% Similarity=0.591 Sum_probs=32.9
Q ss_pred CcceeeeeeeeecccCCCCcEEeccceeccceEeeeccccc
Q psy7583 42 AGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 42 ~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
+-+-|+.+- +||||||++++|+++++||++++.++..+
T Consensus 200 N~iVAvmsy---~GYn~EDAiIink~si~rG~f~s~~~~~~ 237 (599)
T TIGR03670 200 NFVVAVMSY---EGYNIEDALIMNKASIERGLARSTFFRTY 237 (599)
T ss_pred eEEEEEEcc---cCcChhHeeeechhhhhcCCeEEEEEEEE
Confidence 345677777 99999999999999999999999887665
No 22
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 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 polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=91.82 E-value=0.057 Score=56.72 Aligned_cols=46 Identities=57% Similarity=1.014 Sum_probs=42.0
Q ss_pred cCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeecccc
Q psy7583 36 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLR 81 (451)
Q Consensus 36 ~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~ 81 (451)
.++++|+|+|++||||||+|||+||++++|+.+++||++++.++..
T Consensus 71 ~~~e~~~G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~ 116 (386)
T PF00562_consen 71 KFGELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT 116 (386)
T ss_dssp CTTTS-SSEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE
T ss_pred ccccCcceeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE
Confidence 3799999999999999999999999999999999999988877666
No 23
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=89.77 E-value=0.15 Score=59.01 Aligned_cols=37 Identities=43% Similarity=0.940 Sum_probs=32.1
Q ss_pred cceeeeeeeeecccCCCCcEEeccceeccceEeeeccccc
Q psy7583 43 GINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 43 G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
-+-|+.+- +||||||++++|+++++||++++.++..+
T Consensus 480 ~~VAv~~y---~Gyn~EDaiiink~s~~rg~~~s~~~~~~ 516 (866)
T cd00653 480 AIVAVMSY---SGYNFEDAIIINKSSVDRGFFRSIHYKKY 516 (866)
T ss_pred EEEEEecc---ccccccceeeeehhhhhcCceeEEEEEEE
Confidence 45567777 99999999999999999999998887765
No 24
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=89.20 E-value=0.28 Score=61.56 Aligned_cols=56 Identities=36% Similarity=0.584 Sum_probs=44.5
Q ss_pred CCCccceecc--------ccc--cccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEee
Q psy7583 21 YPHKPLVTTR--------SME--YLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRS 76 (451)
Q Consensus 21 yPQ~Plv~T~--------~~~--~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~ 76 (451)
.-|+|+|.-- .+| .....++..|+|..||.|++.|||.||+++++.--+....|.+
T Consensus 785 inQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliSErlv~eD~fTS 850 (2836)
T PRK14844 785 INQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTS 850 (2836)
T ss_pred eeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccCCcccccccccchhhccCceeEE
Confidence 4588999641 122 2456789999999999999999999999999998887776553
No 25
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=89.01 E-value=0.097 Score=61.92 Aligned_cols=38 Identities=34% Similarity=0.676 Sum_probs=33.9
Q ss_pred CcceeeeeeeeecccCCCCcEEeccceeccceEeeeccccc
Q psy7583 42 AGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 42 ~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
+-+-|+.+- +||||||++++|+++++||++++.++..+
T Consensus 704 N~iVAv~sy---~GYn~EDaiIink~s~~rG~~~s~~~~~~ 741 (1103)
T PRK08565 704 NAVVAVLSY---TGYNIEDAIIMNKASIERGLARSTFFRTY 741 (1103)
T ss_pred eEEEEEEcc---cCcchHHhhhhhhhhhhcCCceEEEEEEE
Confidence 456788888 99999999999999999999998887765
No 26
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=87.81 E-value=0.25 Score=58.17 Aligned_cols=78 Identities=24% Similarity=0.430 Sum_probs=70.0
Q ss_pred ccCcccCCcc---------ceEe----------ccCCCccceec----ccccccc------CCCCCCcceeeeeeeeecc
Q psy7583 5 ITNFHVRMDT---------LAHV----------LYYPHKPLVTT----RSMEYLR------FRELPAGINSIVAILCYTG 55 (451)
Q Consensus 5 ~~n~~~R~D~---------~~~~----------L~yPQ~Plv~T----~~~~~~~------~d~~p~G~NaiVAV~sytg 55 (451)
++|+..|.|+ ..|. +.|||+|||+| +..+++. ++++|+|+||+||||||+|
T Consensus 607 ~~~~~~r~d~~~~~~~~~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~G 686 (1065)
T TIGR02013 607 AKRIVIRYDEDEDEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNG 686 (1065)
T ss_pred cceEEEEecCCcccccccceEEEeecccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeec
Confidence 8899999995 4455 45999999999 7888876 9999999999999999999
Q ss_pred cCCCCcEEeccceeccceEeeeccccc
Q psy7583 56 YNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 56 ynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
|||||++++|+.+++||++++.++..+
T Consensus 687 Yn~EDAiiink~~i~rg~~~s~~~~~~ 713 (1065)
T TIGR02013 687 YNYEDAILISERLVKDDVFTSIHIEEY 713 (1065)
T ss_pred ccccceEEeehhhhcCCceEEEEEEEE
Confidence 999999999999999999998887655
No 27
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=87.80 E-value=0.27 Score=58.27 Aligned_cols=47 Identities=30% Similarity=0.531 Sum_probs=43.9
Q ss_pred cCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccccc
Q psy7583 36 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRF 82 (451)
Q Consensus 36 ~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~~ 82 (451)
+++++|+|+||+||||||+||||||++++|+.+++||++++.++..+
T Consensus 709 ~~~e~~~G~N~~VA~~~y~GYn~EDaiiink~si~rg~~~s~~~~~~ 755 (1112)
T PRK00405 709 DNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEY 755 (1112)
T ss_pred CcccccCCcceEEEEEeecccCccceEEEEhhhhccCceEEEEEeee
Confidence 48999999999999999999999999999999999999998876655
No 28
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=79.67 E-value=1.3 Score=56.14 Aligned_cols=53 Identities=25% Similarity=0.436 Sum_probs=41.4
Q ss_pred CCCccceecc--------ccc--cccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccce
Q psy7583 21 YPHKPLVTTR--------SME--YLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGY 73 (451)
Q Consensus 21 yPQ~Plv~T~--------~~~--~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~ 73 (451)
+-|+|+|.-- .+| .....++..|+|..||-|.+.|||.||+++++.--+..-.
T Consensus 775 inqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD~ 837 (2890)
T PRK09603 775 FNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDI 837 (2890)
T ss_pred eeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCcc
Confidence 4588999641 122 2456789999999999999999999999999887665544
No 29
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=79.50 E-value=2 Score=50.44 Aligned_cols=72 Identities=26% Similarity=0.249 Sum_probs=53.3
Q ss_pred EeccCCCccceeccccccccCCCCCCcceeeeeee-----------------------------------------eecc
Q psy7583 17 HVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAIL-----------------------------------------CYTG 55 (451)
Q Consensus 17 ~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~-----------------------------------------sytg 55 (451)
.-|..|..|||.|= +|++...+-. ||+||.- +-||
T Consensus 566 ~~l~~~~~~lv~tG-~E~~~a~e~~---~~~ia~~~~~~~~ve~~~~~I~~~~~~~~~~~~~n~~~~n~~~~~~~~Q~~~ 641 (1060)
T COG0085 566 VPLLRTEAPLVGTG-MEYLDAEDSG---AAVIAKRPGVVTHVEISPIVILGIEASLIPYPEHNQSPYNLYKFARSNQATG 641 (1060)
T ss_pred ccccccccccccCC-ceeecccccc---ceeEeccCCcEEEEeeeeeEEEeeccccCCccccCcChHHHHHHhhhhcccC
Confidence 34778999999997 9988777544 4444421 2267
Q ss_pred cCCCCcEEeccceeccceEeeeccccccccCCCcceE
Q psy7583 56 YNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSI 92 (451)
Q Consensus 56 ynqed~~~~n~~~i~rG~~r~~~~~~~~el~~G~N~~ 92 (451)
+||.+.+.........-.++++++++.+|+|+|+|++
T Consensus 642 ~~~~~~~~~~d~~~~~~~~~~~P~~~~~e~~~GqN~~ 678 (1060)
T COG0085 642 INQRPLVKRGDTVEKGLVYADGPSVDTGELALGQNAL 678 (1060)
T ss_pred CCcccceeccccccccceecCCCccccCcccCCceeE
Confidence 7777777776665555569999999999999999975
No 30
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=78.61 E-value=2.2 Score=30.90 Aligned_cols=27 Identities=19% Similarity=0.315 Sum_probs=21.6
Q ss_pred eeeeccccceEEeecccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.+.|.+||.....+.......|+.|+.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 578999999877665555788999985
No 31
>KOG0215|consensus
Probab=77.67 E-value=0.75 Score=51.90 Aligned_cols=47 Identities=26% Similarity=0.550 Sum_probs=39.7
Q ss_pred cccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeecccc
Q psy7583 32 MEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLR 81 (451)
Q Consensus 32 ~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~~ 81 (451)
.++-.+..=.+++-||.+- +||+.||++.+|+++++||+.|+..|.+
T Consensus 749 i~ydKLPAGQNAtVAVMSY---SGYDIEDALVLNKsSlDRGfGRC~Vyk~ 795 (1153)
T KOG0215|consen 749 INYDKLPAGQNATVAVMSY---SGYDIEDALVLNKSSIDRGFGRCEVYKK 795 (1153)
T ss_pred eccccCCCCCccEEEEEec---cCCchhhhhhcccchhccCcceEEEEee
Confidence 3444455556889999999 9999999999999999999999888765
No 32
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=75.63 E-value=5.2 Score=44.85 Aligned_cols=54 Identities=19% Similarity=0.302 Sum_probs=36.0
Q ss_pred eEEecCCcceEEEEEEEEec-cCCeeEEEEEEeecCCCccccccccccCCccEEe
Q psy7583 206 STFLRNSETGIVDQVMLTLN-VDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCG 259 (451)
Q Consensus 206 s~~~~~~e~g~Vd~V~i~~~-~~g~~~vkv~ir~~R~p~IGDKFsSRHGQKGvvs 259 (451)
.+.++....-.|++|.-... .++.-.+|+++-..=.=--|=|.||-||||||.-
T Consensus 681 YmYfR~~~~Q~ve~l~sem~~~nd~v~vKl~~V~st~dLeGlKICgIHGQKGVln 735 (748)
T PF04941_consen 681 YMYFRKVKGQRVEKLDSEMTCINDTVYVKLTLVTSTSDLEGLKICGIHGQKGVLN 735 (748)
T ss_pred EEEEEecCCEEEEEEeeEEEEeCCEEEEEEEEEEEecCccceEEeeeeccccccc
Confidence 34556666667776642211 2345567777666556667999999999999974
No 33
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=75.46 E-value=6.1 Score=44.88 Aligned_cols=54 Identities=20% Similarity=0.320 Sum_probs=35.3
Q ss_pred EEecCCcceEEEEEEEEec-cCCeeEEEEEEeecCCCccccccccccCCccEEee
Q psy7583 207 TFLRNSETGIVDQVMLTLN-VDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGI 260 (451)
Q Consensus 207 ~~~~~~e~g~Vd~V~i~~~-~~g~~~vkv~ir~~R~p~IGDKFsSRHGQKGvvs~ 260 (451)
+.++....-.|++|.-..+ .+..-.+|+++-..=.=-.|=|.||=||||||+..
T Consensus 672 mYfR~~~~Q~ie~l~s~m~~~nd~v~lKl~~Vtst~dLeGlKICgIHGQKGVln~ 726 (865)
T PHA03394 672 VYFRQIKNQRIERLDSEMTVINDTVYLKIRLVTSTSDLEGLKICGIHGQKGVLNG 726 (865)
T ss_pred EEEEecCCeEEEEEeeEEEEcCCEEEEEEEEEEEecCcceeEEeeecccccccCC
Confidence 4455556666777643222 22244567766555555679999999999999864
No 34
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=75.23 E-value=1.7 Score=29.43 Aligned_cols=26 Identities=27% Similarity=0.543 Sum_probs=19.4
Q ss_pred eeeeccccceEEeecccceeEeccCCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
.|+|..||-+.. .....+.|+.|+..
T Consensus 1 ~~~C~~CGy~y~--~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYD--GEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEEC--CCcCCCcCcCCCCc
Confidence 378999998743 33467889999864
No 35
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=74.98 E-value=2.6 Score=33.59 Aligned_cols=49 Identities=24% Similarity=0.444 Sum_probs=29.4
Q ss_pred eeeeeeccccceEEeecccceeEeccCCCCCccceecC------chhHHHHHHHHHh
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRL------PYAAKLLFQELMS 441 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~i------Py~~klL~~EL~s 441 (451)
|.++.| .||..++......+..| .|+..-+|....| -.-..-+.++||.
T Consensus 1 ylifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~rIl~~~~~~~eA~eiVrklQ~ 55 (68)
T PF09082_consen 1 YLIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERRILARAENAEEASEIVRKLQE 55 (68)
T ss_dssp EEEEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS-BS--SSHHHHHHHHHHHSS
T ss_pred CEEEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEEEEEecCCHHHHHHHHHHHHH
Confidence 357889 79999998777778889 8997666655554 2233455566653
No 36
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=73.46 E-value=4.3 Score=29.46 Aligned_cols=37 Identities=24% Similarity=0.697 Sum_probs=24.9
Q ss_pred HHHHHhhcccCCceeeeeeccccceEEeeccc-ceeEeccCCC
Q psy7583 378 QFLRERLFEVSDPYRIHVCNFCGLIAIANMRN-NTFECKGCKN 419 (451)
Q Consensus 378 ~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~-~~~~C~~C~~ 419 (451)
..|.+..+-.- .+|+.||...++..+. ..|.|..|+.
T Consensus 8 ~~l~~~RW~~g-----~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 8 EYLEEIRWPDG-----FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred HHHHHhcCCCC-----CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 34555554322 6799999986655444 7889999973
No 37
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=71.86 E-value=2.5 Score=35.24 Aligned_cols=28 Identities=29% Similarity=0.873 Sum_probs=23.2
Q ss_pred eeeeeccccceEEeecccceeEeccCCC
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.-++|+.||...+.-...+.|.|..|+.
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGA 61 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCC
Confidence 4578999999977656678999999984
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=70.52 E-value=2 Score=33.25 Aligned_cols=31 Identities=19% Similarity=0.502 Sum_probs=17.9
Q ss_pred CceeeeeeccccceEEeecccceeEeccCCC
Q psy7583 389 DPYRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 389 D~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+.....+|..||..+....+.-.|.|+.|+.
T Consensus 3 ~~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccccCccccCCCCcccCCCccCEeeCCCCCC
Confidence 3344556777776665333344566777753
No 39
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=68.60 E-value=3.3 Score=28.37 Aligned_cols=26 Identities=27% Similarity=0.645 Sum_probs=18.7
Q ss_pred eeeeccccceEEeecccceeEeccCCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
.|+|..||-+.... .....|+.|+..
T Consensus 2 ~~~C~~CG~i~~g~--~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGE--EAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECC--cCCCcCcCCCCc
Confidence 58999999885432 234579999864
No 40
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=67.73 E-value=3.2 Score=26.44 Aligned_cols=23 Identities=26% Similarity=0.678 Sum_probs=16.1
Q ss_pred eccccceEEeecccceeEeccCC
Q psy7583 396 CNFCGLIAIANMRNNTFECKGCK 418 (451)
Q Consensus 396 C~~CG~~~~~~~~~~~~~C~~C~ 418 (451)
|..||..+..-.+...|.|+.|+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 77888776643335578899886
No 41
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=63.96 E-value=5.4 Score=35.83 Aligned_cols=24 Identities=21% Similarity=0.519 Sum_probs=20.1
Q ss_pred eeeccccceEEeecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.-|+.||+.++. +++.-+|+.|+.
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCccee--eCCeEECCCCCc
Confidence 459999999986 567778999984
No 42
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.71 E-value=3.8 Score=38.30 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=19.1
Q ss_pred eeeeccccceEEeecccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+|||..||-+... .....|+.|+.
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 8999999988654 23567999984
No 43
>KOG0216|consensus
Probab=60.36 E-value=3.7 Score=46.80 Aligned_cols=34 Identities=35% Similarity=0.634 Sum_probs=29.6
Q ss_pred CCCCCcceeeeeeeeecccCCCCcEEeccceeccceE
Q psy7583 38 RELPAGINSIVAILCYTGYNQEDSVILNASAVERGYF 74 (451)
Q Consensus 38 d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~ 74 (451)
..=-+.+-||++- |||++||++++|+++++||+.
T Consensus 720 p~GtNaiVAVisy---TgyDMeDAmiiNK~s~eRGf~ 753 (1111)
T KOG0216|consen 720 PNGTNAIVAVISY---TGYDMEDAMIINKSSYERGFA 753 (1111)
T ss_pred CCCcceEEEEEee---cccChhhhhhhchhhhhcccc
Confidence 3344678899999 999999999999999999973
No 44
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=58.25 E-value=10 Score=25.93 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=21.6
Q ss_pred eeeeccccceEEeecccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.+.|+.||.....+..+....|..|+.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 367999999887766667778999974
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=58.02 E-value=6.5 Score=28.76 Aligned_cols=25 Identities=28% Similarity=0.771 Sum_probs=16.3
Q ss_pred eeccccceEEeec-cc-ceeEeccCCC
Q psy7583 395 VCNFCGLIAIANM-RN-NTFECKGCKN 419 (451)
Q Consensus 395 vC~~CG~~~~~~~-~~-~~~~C~~C~~ 419 (451)
.|+.||.++.... .. ..++|+.|+-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCC
Confidence 4888888776432 12 3678888874
No 46
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=57.95 E-value=9.1 Score=32.21 Aligned_cols=29 Identities=24% Similarity=0.700 Sum_probs=22.7
Q ss_pred eeeeeeccccceEEeecccceeEeccCCC
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+.-+.|+.||.....-...+.|.|..|+.
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGK 61 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTE
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCC
Confidence 45688999999987555568899999984
No 47
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=57.79 E-value=11 Score=26.89 Aligned_cols=25 Identities=20% Similarity=0.558 Sum_probs=17.8
Q ss_pred eeeccccceE-EeecccceeEeccCC
Q psy7583 394 HVCNFCGLIA-IANMRNNTFECKGCK 418 (451)
Q Consensus 394 ~vC~~CG~~~-~~~~~~~~~~C~~C~ 418 (451)
++|+.||.-. ..+..++.++|..|+
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCC
Confidence 4688998864 445666778899996
No 48
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=56.53 E-value=8.3 Score=36.64 Aligned_cols=35 Identities=23% Similarity=0.581 Sum_probs=27.3
Q ss_pred eeeccccceEEeecccceeEeccCCCCCccceecCchh
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYA 431 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~ 431 (451)
-.|++|+..+.. +.....|+.|+. ++..++..||-
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~-tEkRKia~~y~ 184 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN-TEKRKIAKDYG 184 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC-EEeeeeccccc
Confidence 579999999876 345678999985 57778888774
No 49
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.49 E-value=7.1 Score=36.77 Aligned_cols=45 Identities=20% Similarity=0.363 Sum_probs=32.4
Q ss_pred cchhHHHHHhhcccCCceeeeeeccccceEEee-cccceeEeccCCC
Q psy7583 374 HGAAQFLRERLFEVSDPYRIHVCNFCGLIAIAN-MRNNTFECKGCKN 419 (451)
Q Consensus 374 ~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~-~~~~~~~C~~C~~ 419 (451)
|-...-|++++-..++. ..++|+.||.-.... .-...|.|+.|+.
T Consensus 99 ~~~~~klk~~l~~e~~~-~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~ 144 (178)
T PRK06266 99 MEELKKLKEQLEEEENN-MFFFCPNCHIRFTFDEAMEYGFRCPQCGE 144 (178)
T ss_pred HHHHHHHHHHhhhccCC-CEEECCCCCcEEeHHHHhhcCCcCCCCCC
Confidence 45567788898777766 579999999665432 1234689999985
No 50
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=52.64 E-value=11 Score=28.14 Aligned_cols=29 Identities=17% Similarity=0.344 Sum_probs=21.8
Q ss_pred eeeeeeccccceEEeecccceeEeccCCC
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
...++|..||.............|+.|+.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 35789999999875444455668999985
No 51
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=52.06 E-value=10 Score=34.63 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=21.8
Q ss_pred eeeeccccceEEeecccceeEeccCCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
.++|.+||.............|+.|+..
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 5799999988776554556679999864
No 52
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=50.81 E-value=9.4 Score=34.50 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=25.8
Q ss_pred CceeeeeeccccceEEeecccceeEeccCCCCCccceecCc
Q psy7583 389 DPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLP 429 (451)
Q Consensus 389 D~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iP 429 (451)
.....-.|.+||...+.- ...|..|.+..++..+++|
T Consensus 25 ~kl~g~kC~~CG~v~~PP----r~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPP----RAYCPKCGSETELEWVELS 61 (140)
T ss_pred CcEEEEEcCCCCeEEcCC----cccCCCCCCCCceEEEEeC
Confidence 345667899999987642 2359999987655556554
No 53
>PRK00420 hypothetical protein; Validated
Probab=49.37 E-value=11 Score=33.05 Aligned_cols=25 Identities=20% Similarity=0.468 Sum_probs=19.5
Q ss_pred eeeccccceEEeecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
..|+.||...... +++...|+.|+.
T Consensus 24 ~~CP~Cg~pLf~l-k~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFEL-KDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceec-CCCceECCCCCC
Confidence 4599999988753 456778999985
No 54
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=47.40 E-value=6.7 Score=42.01 Aligned_cols=54 Identities=31% Similarity=0.588 Sum_probs=34.3
Q ss_pred HhhcccCCc--eeeeeeccccceEEeecccceeEeccCCCCCccceec--CchhHHHHHHHHH
Q psy7583 382 ERLFEVSDP--YRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVR--LPYAAKLLFQELM 440 (451)
Q Consensus 382 e~l~~~SD~--~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~--iPy~~klL~~EL~ 440 (451)
|.-...||+ ...|-|.+||.+.-.|. ...| .|++..++..+. .| |.+.|+-||-
T Consensus 117 eqyhyas~k~~va~w~c~~cg~~iean~---kp~c-~cg~~~~~~ei~gs~p-asrf~i~el~ 174 (593)
T COG2401 117 EQYHYASQKEKVALWRCEKCGTIIEANT---KPEC-KCGSHVHILEIKGSTP-ASRFLIVELV 174 (593)
T ss_pred HHhhhccccceEEEEecchhchhhhhcC---Cccc-CCCCceEEEEeecCCc-chheeeeehh
Confidence 334445654 45699999999876653 3479 888643333322 36 7788877774
No 55
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=46.88 E-value=12 Score=33.84 Aligned_cols=42 Identities=19% Similarity=0.320 Sum_probs=27.5
Q ss_pred hHHHHHhhcccCCceeeeeeccccceEEee------cccceeEeccCCC
Q psy7583 377 AQFLRERLFEVSDPYRIHVCNFCGLIAIAN------MRNNTFECKGCKN 419 (451)
Q Consensus 377 ~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~------~~~~~~~C~~C~~ 419 (451)
..-|++++-..++. ..++|+.||...... -..+.|.|+.|+.
T Consensus 84 ~~~L~~~l~~e~~~-~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 84 RKRLEDKLEDETNN-AYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGE 131 (147)
T ss_pred HHHHHHHHhcccCC-cEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCC
Confidence 34567777655554 379999999664431 1134499999985
No 56
>PRK11032 hypothetical protein; Provisional
Probab=46.43 E-value=16 Score=34.04 Aligned_cols=28 Identities=18% Similarity=0.231 Sum_probs=21.8
Q ss_pred eeeeccccceEEeecccceeEeccCCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
..||.+||............-|+.|+..
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 5699999988776655556679999864
No 57
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=46.25 E-value=19 Score=26.13 Aligned_cols=26 Identities=23% Similarity=0.626 Sum_probs=19.0
Q ss_pred eeeeccccceEEeecccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.++|.+||...... ......|+.|+.
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCc
Confidence 48999999875433 345668999985
No 58
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=45.79 E-value=12 Score=34.56 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=30.6
Q ss_pred cchhHHHHHhhcccCCceeeeeeccccceEEee-cccceeEeccCCC
Q psy7583 374 HGAAQFLRERLFEVSDPYRIHVCNFCGLIAIAN-MRNNTFECKGCKN 419 (451)
Q Consensus 374 ~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~-~~~~~~~C~~C~~ 419 (451)
|.....|+++|-..++.. .++|+.|+.-.... .-...|.|+.|++
T Consensus 91 ~~~~~~lk~~l~~e~~~~-~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~ 136 (158)
T TIGR00373 91 EETAKKLREKLEFETNNM-FFICPNMCVRFTFNEAMELNFTCPRCGA 136 (158)
T ss_pred HHHHHHHHHHHhhccCCC-eEECCCCCcEeeHHHHHHcCCcCCCCCC
Confidence 455667788887665554 68999999654432 1134689999985
No 59
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=44.98 E-value=13 Score=31.42 Aligned_cols=29 Identities=24% Similarity=0.630 Sum_probs=22.5
Q ss_pred eeeeeeccccceEEeecccceeEeccCCC
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+..+.|+.||.....-...+.|.|..|+.
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 45678999998776544567899999984
No 60
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 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. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=44.53 E-value=16 Score=25.14 Aligned_cols=26 Identities=19% Similarity=0.627 Sum_probs=16.7
Q ss_pred eeeccccceEEeec-ccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIANM-RNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~~~-~~~~~~C~~C~~ 419 (451)
..|++||.++.... +.....|+.|.-
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 46999999987532 122227999974
No 61
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=44.46 E-value=17 Score=25.33 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=19.2
Q ss_pred eeccccceEEeecccceeEeccCCC
Q psy7583 395 VCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 395 vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.|..||.. ......+.++|..|+.
T Consensus 10 ~C~~C~~~-~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR-WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe-EeEccCCEEEhhhCce
Confidence 39999999 5556678899999974
No 62
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=44.11 E-value=19 Score=25.90 Aligned_cols=24 Identities=21% Similarity=0.638 Sum_probs=18.0
Q ss_pred eeeccccceEEeecccceeEeccCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCK 418 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~ 418 (451)
..|..||.++..+ +++...|..|+
T Consensus 18 ~~Cp~C~~PL~~~-k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRD-KDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEe-cCCCEECCCCC
Confidence 4599999998874 35566799884
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.67 E-value=19 Score=28.08 Aligned_cols=27 Identities=26% Similarity=0.565 Sum_probs=17.7
Q ss_pred eeeeccccceEEeecccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
..+|+.||..+......-.|.|+.|++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCc
Confidence 467888887765444444677777763
No 64
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.37 E-value=17 Score=30.66 Aligned_cols=29 Identities=28% Similarity=0.722 Sum_probs=22.4
Q ss_pred eeeeeeccccceEEeecccceeEeccCCC
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+.-+.|+.||.....-.-.+.|.|..|+.
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PRK03976 34 RAKHVCPVCGRPKVKRVGTGIWECRKCGA 62 (90)
T ss_pred hcCccCCCCCCCceEEEEEEEEEcCCCCC
Confidence 45678999998876544467899999984
No 65
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=40.24 E-value=16 Score=30.81 Aligned_cols=30 Identities=33% Similarity=0.738 Sum_probs=22.6
Q ss_pred ceeeeeeccccceEEeecccceeEeccCCC
Q psy7583 390 PYRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 390 ~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
.+..+.|+.||.....-...+.|.|..|+.
T Consensus 33 q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PTZ00255 33 QHAKYFCPFCGKHAVKRQAVGIWRCKGCKK 62 (90)
T ss_pred HhCCccCCCCCCCceeeeeeEEEEcCCCCC
Confidence 345678999998766544457899999984
No 66
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=39.42 E-value=14 Score=32.17 Aligned_cols=28 Identities=18% Similarity=0.564 Sum_probs=20.5
Q ss_pred eeeeeccccceEEeecccceeEeccCCCC
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
+-++|.+||.-.+ ...+..-+|+.|+..
T Consensus 8 tKR~Cp~CG~kFY-DLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 8 TKRTCPSCGAKFY-DLNKDPIVCPKCGTE 35 (108)
T ss_pred CcccCCCCcchhc-cCCCCCccCCCCCCc
Confidence 3479999997654 444566689999864
No 67
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=39.32 E-value=23 Score=23.91 Aligned_cols=25 Identities=20% Similarity=0.539 Sum_probs=20.8
Q ss_pred eeccccceEEeecccceeEeccCCC
Q psy7583 395 VCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 395 vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+|..|+.++.+......+.|..|..
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 6999999998876667889999974
No 68
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=38.08 E-value=22 Score=35.81 Aligned_cols=24 Identities=29% Similarity=0.534 Sum_probs=18.4
Q ss_pred eeccccceEEee--cccceeEeccCC
Q psy7583 395 VCNFCGLIAIAN--MRNNTFECKGCK 418 (451)
Q Consensus 395 vC~~CG~~~~~~--~~~~~~~C~~C~ 418 (451)
-|..||...... ...++|+|+.|.
T Consensus 247 pC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 799999987643 234688999996
No 69
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.94 E-value=20 Score=27.79 Aligned_cols=28 Identities=21% Similarity=0.503 Sum_probs=21.7
Q ss_pred eeeeeccccceEEeecccceeEeccCCC
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+...|+.||...........+.|+.|+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCC
Confidence 5678999998866544566889999974
No 70
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=34.11 E-value=41 Score=22.36 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=14.4
Q ss_pred eeeccccceEEeecccceeEeccCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCK 418 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~ 418 (451)
..|..||...........-.|+.|+
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS
T ss_pred cccCcCCccccCCCCcCEeECCCCc
Confidence 4699999988766544456788886
No 71
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=34.09 E-value=21 Score=25.15 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=14.4
Q ss_pred eeeccccceEE----eecccceeEeccCCCC
Q psy7583 394 HVCNFCGLIAI----ANMRNNTFECKGCKNK 420 (451)
Q Consensus 394 ~vC~~CG~~~~----~~~~~~~~~C~~C~~~ 420 (451)
..|..|+.++. .+...+.|.|.+|+..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 35888987753 2334568999999853
No 72
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.70 E-value=15 Score=30.94 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=18.4
Q ss_pred eeeccccceEEeecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
..|.+||.-...+.-+..-.|+.|++
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKS 84 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKS 84 (97)
T ss_pred hhhcccCccccccccCCcccCCcchh
Confidence 58999997654433344568999985
No 73
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=32.01 E-value=28 Score=23.62 Aligned_cols=25 Identities=20% Similarity=0.600 Sum_probs=15.8
Q ss_pred eeeccccceEEeecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
++|.+||...... ....-.|+.|+.
T Consensus 1 Y~C~~Cg~~~~~~-~~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELK-PGDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE-BS-TSSTSSBSSSS-
T ss_pred CCCCcCCCeeEcC-CCCcEECCcCCC
Confidence 5799999876532 233457999974
No 74
>KOG3507|consensus
Probab=31.86 E-value=33 Score=26.66 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=19.2
Q ss_pred eeeeeccccceEEeecccceeEeccCC
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCK 418 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~ 418 (451)
.++||..||.--.. .+.....|+.|+
T Consensus 19 miYiCgdC~~en~l-k~~D~irCReCG 44 (62)
T KOG3507|consen 19 MIYICGDCGQENTL-KRGDVIRCRECG 44 (62)
T ss_pred EEEEeccccccccc-cCCCcEehhhcc
Confidence 57999999976432 235677899997
No 75
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=31.09 E-value=35 Score=26.24 Aligned_cols=24 Identities=33% Similarity=0.730 Sum_probs=17.6
Q ss_pred eeeeeccccceEEeecccceeEeccCCCCC
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCKNKT 421 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~ 421 (451)
.+..|..||..... ..|+.|+..+
T Consensus 4 ~mr~C~~CgvYTLk------~~CP~CG~~t 27 (56)
T PRK13130 4 KIRKCPKCGVYTLK------EICPVCGGKT 27 (56)
T ss_pred cceECCCCCCEEcc------ccCcCCCCCC
Confidence 46789999987542 3599998653
No 76
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=30.99 E-value=24 Score=31.59 Aligned_cols=28 Identities=7% Similarity=0.072 Sum_probs=20.9
Q ss_pred eeeeeccccceEEeecccceeEeccCCCC
Q psy7583 392 RIHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 392 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
+-++|.+||.-.+ ...+...+|+.|+..
T Consensus 8 tKr~Cp~cg~kFY-DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFY-DLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCcccc-ccCCCCccCCCcCCc
Confidence 4579999998654 455567789999853
No 77
>PF14353 CpXC: CpXC protein
Probab=28.82 E-value=16 Score=32.08 Aligned_cols=40 Identities=20% Similarity=0.215 Sum_probs=32.0
Q ss_pred chhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEe
Q psy7583 364 GEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIA 405 (451)
Q Consensus 364 GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~ 405 (451)
++.|.|-++.-....-++|+++ +..+..++|+.||.....
T Consensus 11 ~~~~v~~~I~~~~~p~l~e~il--~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 11 FEFEVWTSINADEDPELKEKIL--DGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred eEEEEEeEEcCcCCHHHHHHHH--cCCcCEEECCCCCCceec
Confidence 5677888888888888999987 566778999999977643
No 78
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=28.43 E-value=39 Score=34.15 Aligned_cols=31 Identities=29% Similarity=0.582 Sum_probs=21.1
Q ss_pred cCCceeeeeeccccceEEeecccceeEeccCCCCCcc
Q psy7583 387 VSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQI 423 (451)
Q Consensus 387 ~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~ 423 (451)
..|+. ++|.+||.... .-.+.|+.|++=..+
T Consensus 350 ~~~p~--~~c~~cg~~~~----~~~~~c~~c~~~~~~ 380 (389)
T PRK11788 350 KRKPR--YRCRNCGFTAR----TLYWHCPSCKAWETI 380 (389)
T ss_pred hCCCC--EECCCCCCCCc----cceeECcCCCCccCc
Confidence 44554 88999998632 235689999864443
No 79
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=27.95 E-value=50 Score=22.65 Aligned_cols=27 Identities=19% Similarity=0.321 Sum_probs=17.9
Q ss_pred eeeeccccceEEeec---ccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIANM---RNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~---~~~~~~C~~C~~ 419 (451)
.+.|.+||....... ......|+.|+.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 468999998643221 133557999985
No 80
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=27.89 E-value=34 Score=23.76 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=16.4
Q ss_pred eeeccccceEEe--ecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIA--NMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~--~~~~~~~~C~~C~~ 419 (451)
++|.+||.+-+. ++....-.|-.|+.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 689999988653 22223346888874
No 81
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.87 E-value=53 Score=22.59 Aligned_cols=24 Identities=21% Similarity=0.558 Sum_probs=11.4
Q ss_pred eeccccceEEeec----ccceeEeccCC
Q psy7583 395 VCNFCGLIAIANM----RNNTFECKGCK 418 (451)
Q Consensus 395 vC~~CG~~~~~~~----~~~~~~C~~C~ 418 (451)
.|+.||..+.... ....++|..|+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred ccccccChhhhhcCCCCCccceECCCCC
Confidence 4888887765421 23356788886
No 82
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=27.18 E-value=45 Score=24.45 Aligned_cols=15 Identities=27% Similarity=0.516 Sum_probs=13.4
Q ss_pred CcccCcEEeCCCEEE
Q psy7583 166 IIAPGLRVSGDDVVI 180 (451)
Q Consensus 166 i~~vG~~v~~gDili 180 (451)
.+..|+.|+.||+|+
T Consensus 17 ~V~~G~~VkkGd~L~ 31 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLL 31 (50)
T ss_pred EecCCCEEcCCCEEE
Confidence 477899999999997
No 83
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=26.83 E-value=56 Score=22.32 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=14.6
Q ss_pred eeeeeeccccceEEeecccceeEeccCCC
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
..+..|..||.+.+.- ...|+.|.+
T Consensus 9 l~~~rC~~Cg~~~~pP----r~~Cp~C~s 33 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPP----RPVCPHCGS 33 (37)
T ss_dssp EEEEE-TTT--EEES------SEETTTT-
T ss_pred EEEEEcCCCCCEecCC----CcCCCCcCc
Confidence 3567899999987642 246999974
No 84
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.65 E-value=38 Score=35.21 Aligned_cols=41 Identities=24% Similarity=0.499 Sum_probs=27.2
Q ss_pred HHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceec
Q psy7583 379 FLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVR 427 (451)
Q Consensus 379 ~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~ 427 (451)
.+.|++-.+ ..|.|.+||.-++. -.|.|+.|+.=..++++.
T Consensus 344 mvge~l~~~----~~YRC~~CGF~a~~----l~W~CPsC~~W~TikPir 384 (389)
T COG2956 344 MVGEQLRRK----PRYRCQNCGFTAHT----LYWHCPSCRAWETIKPIR 384 (389)
T ss_pred HHHHHHhhc----CCceecccCCccee----eeeeCCCcccccccCCcc
Confidence 344555433 34779999987653 368899999766665543
No 85
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=26.42 E-value=38 Score=26.29 Aligned_cols=25 Identities=28% Similarity=0.753 Sum_probs=17.5
Q ss_pred eeeeccccceEEeecccceeEeccCCCCCcc
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKNKTQI 423 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~ 423 (451)
++.|.+||...-.+ .|+.|+..+.+
T Consensus 5 ~rkC~~cg~YTLke------~Cp~CG~~t~~ 29 (59)
T COG2260 5 IRKCPKCGRYTLKE------KCPVCGGDTKV 29 (59)
T ss_pred hhcCcCCCceeecc------cCCCCCCcccc
Confidence 46899999865432 59999865433
No 86
>PHA00626 hypothetical protein
Probab=25.85 E-value=53 Score=25.34 Aligned_cols=24 Identities=21% Similarity=0.516 Sum_probs=15.7
Q ss_pred eeccccce-EEee----cccceeEeccCC
Q psy7583 395 VCNFCGLI-AIAN----MRNNTFECKGCK 418 (451)
Q Consensus 395 vC~~CG~~-~~~~----~~~~~~~C~~C~ 418 (451)
.|++||+- .+.. ...+.|.|+.|+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCG 30 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCG 30 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCC
Confidence 48899983 2221 124678899997
No 87
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=25.49 E-value=23 Score=35.78 Aligned_cols=26 Identities=23% Similarity=0.575 Sum_probs=20.4
Q ss_pred eeeccccceEEe-ecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIA-NMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~-~~~~~~~~C~~C~~ 419 (451)
.-|+.||.+.+. +...+.++|+.|+-
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp~c~~ 55 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCPKCGH 55 (294)
T ss_pred eECCCccceeeHHHHHhhhhcccccCc
Confidence 359999999874 45667889999984
No 88
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=25.19 E-value=71 Score=22.68 Aligned_cols=27 Identities=19% Similarity=0.392 Sum_probs=17.3
Q ss_pred eeeeccccceEEee---cccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIAN---MRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~---~~~~~~~C~~C~~ 419 (451)
-+.|.+||...... .......|+.|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 47899999543221 1234557999986
No 89
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=24.68 E-value=47 Score=35.75 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=20.2
Q ss_pred eeeeeeccccceEEeecccceeEeccCCCCCcc
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKNKTQI 423 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~ 423 (451)
...|+|.+||.-.. +-.|.|+.|+.=..+
T Consensus 5 ~~~y~C~~Cg~~~~----~~~g~Cp~C~~w~t~ 33 (454)
T TIGR00416 5 KSKFVCQHCGADSP----KWQGKCPACHAWNTI 33 (454)
T ss_pred CCeEECCcCCCCCc----cccEECcCCCCcccc
Confidence 35799999997532 335689999864333
No 90
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.68 E-value=34 Score=21.79 Aligned_cols=22 Identities=23% Similarity=0.486 Sum_probs=14.4
Q ss_pred eeeccccceEEeecccceeEeccCCC
Q psy7583 394 HVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
..|.+||.... .+...|+.|+.
T Consensus 3 ~~Cp~Cg~~~~----~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEID----PDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCC----cccccChhhCC
Confidence 46999998532 22335999974
No 91
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.20 E-value=54 Score=32.82 Aligned_cols=24 Identities=17% Similarity=0.346 Sum_probs=17.6
Q ss_pred eeccccceEEee--cccceeEeccCC
Q psy7583 395 VCNFCGLIAIAN--MRNNTFECKGCK 418 (451)
Q Consensus 395 vC~~CG~~~~~~--~~~~~~~C~~C~ 418 (451)
-|..||...... ....+|+|+.|.
T Consensus 246 pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCCeeEEEEECCCccEECcCCc
Confidence 699999876432 234688999996
No 92
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.94 E-value=44 Score=24.95 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=17.8
Q ss_pred eeeeccccc-eEEeecccceeEeccCC
Q psy7583 393 IHVCNFCGL-IAIANMRNNTFECKGCK 418 (451)
Q Consensus 393 ~~vC~~CG~-~~~~~~~~~~~~C~~C~ 418 (451)
...|++||. +.... .+.+.|..|+
T Consensus 20 ~~fCP~Cg~~~m~~~--~~r~~C~~Cg 44 (50)
T PRK00432 20 NKFCPRCGSGFMAEH--LDRWHCGKCG 44 (50)
T ss_pred cCcCcCCCcchhecc--CCcEECCCcC
Confidence 358999999 65543 3678899997
No 93
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.82 E-value=1.3e+02 Score=21.92 Aligned_cols=46 Identities=17% Similarity=0.361 Sum_probs=26.2
Q ss_pred eeeccccceEEeecc---cceeEeccCCCCC-cc--ceecCchhHHHHHHHH
Q psy7583 394 HVCNFCGLIAIANMR---NNTFECKGCKNKT-QI--SQVRLPYAAKLLFQEL 439 (451)
Q Consensus 394 ~vC~~CG~~~~~~~~---~~~~~C~~C~~~~-~~--~~v~iPy~~klL~~EL 439 (451)
-+|..||.......+ ...|.|..+.... .. ..+.....-+.++++|
T Consensus 6 l~C~~CG~~m~~~~~~~~~~yy~C~~~~~~~~~C~~~~i~~~~ie~~v~~~l 57 (58)
T PF13408_consen 6 LRCGHCGSKMTRRKRKGKYRYYRCSNRRRKGKGCPNKSIREEEIEEAVLEAL 57 (58)
T ss_pred EEcccCCcEeEEEECCCCceEEEcCCCcCCCCCCCCCEeCHHHHHHHHHHHh
Confidence 579999988765432 2356788775433 22 2344444555555554
No 94
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=23.43 E-value=81 Score=22.97 Aligned_cols=27 Identities=19% Similarity=0.316 Sum_probs=16.8
Q ss_pred eeeeccccceEEee---cccceeEeccCCC
Q psy7583 393 IHVCNFCGLIAIAN---MRNNTFECKGCKN 419 (451)
Q Consensus 393 ~~vC~~CG~~~~~~---~~~~~~~C~~C~~ 419 (451)
.+.|.+||...... .......|+.|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 47899999843221 1123446999986
No 95
>KOG0402|consensus
Probab=23.14 E-value=26 Score=29.14 Aligned_cols=49 Identities=18% Similarity=0.410 Sum_probs=29.5
Q ss_pred eeeeccccceEEeecccceeEeccCCCCCc--cceecCc--hhHHHHHHHHHh
Q psy7583 393 IHVCNFCGLIAIANMRNNTFECKGCKNKTQ--ISQVRLP--YAAKLLFQELMS 441 (451)
Q Consensus 393 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~--~~~v~iP--y~~klL~~EL~s 441 (451)
-+.|+.||.....-.-.+.|.|..|+.... ...+.-| -+++..+.-|..
T Consensus 36 ky~CsfCGK~~vKR~AvGiW~C~~C~kv~agga~~~~t~aa~t~rs~irrlre 88 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKAVGIWKCGSCKKVVAGGAYTVTTAAAATVRSTIRRLRE 88 (92)
T ss_pred hhhhhhcchhhhhhhceeEEecCCccceeccceEEeccchhHHHHHHHHHHHH
Confidence 467999998866444457899999974211 1122333 556666665553
No 96
>PRK10445 endonuclease VIII; Provisional
Probab=23.13 E-value=58 Score=32.40 Aligned_cols=24 Identities=29% Similarity=0.702 Sum_probs=17.4
Q ss_pred eeccccceEEee--cccceeEeccCC
Q psy7583 395 VCNFCGLIAIAN--MRNNTFECKGCK 418 (451)
Q Consensus 395 vC~~CG~~~~~~--~~~~~~~C~~C~ 418 (451)
-|..||...... ....+|+|+.|.
T Consensus 237 ~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 237 ACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCEeEEEEECCCCcEECCCCc
Confidence 499999876532 234688899996
No 97
>PRK12495 hypothetical protein; Provisional
Probab=22.56 E-value=41 Score=32.87 Aligned_cols=31 Identities=16% Similarity=0.351 Sum_probs=22.5
Q ss_pred cCCceeeeeeccccceEEeecccceeEeccCCC
Q psy7583 387 VSDPYRIHVCNFCGLIAIANMRNNTFECKGCKN 419 (451)
Q Consensus 387 ~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~ 419 (451)
+......+.|..||..+.. ..+.-+|..|..
T Consensus 36 ~gatmsa~hC~~CG~PIpa--~pG~~~Cp~CQ~ 66 (226)
T PRK12495 36 QGATMTNAHCDECGDPIFR--HDGQEFCPTCQQ 66 (226)
T ss_pred hhcccchhhcccccCcccC--CCCeeECCCCCC
Confidence 4455567889999998773 245667999974
No 98
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=21.89 E-value=93 Score=24.31 Aligned_cols=30 Identities=20% Similarity=0.433 Sum_probs=25.1
Q ss_pred eeeeeeccccceEEeecccceeEeccCCCC
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
.++-+|..|.-.+.++...+..+|+.|+-.
T Consensus 6 LeiLaCP~~kg~L~~~~~~~~L~c~~~~~a 35 (60)
T COG2835 6 LEILACPVCKGPLVYDEEKQELICPRCKLA 35 (60)
T ss_pred heeeeccCcCCcceEeccCCEEEecccCce
Confidence 357899999999888877788899999853
No 99
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=21.87 E-value=67 Score=32.09 Aligned_cols=25 Identities=28% Similarity=0.538 Sum_probs=17.7
Q ss_pred eeccccceEEee--cccceeEeccCCC
Q psy7583 395 VCNFCGLIAIAN--MRNNTFECKGCKN 419 (451)
Q Consensus 395 vC~~CG~~~~~~--~~~~~~~C~~C~~ 419 (451)
-|..||...... ....+|+|+.|..
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 499999775432 2246889999974
No 100
>PRK11823 DNA repair protein RadA; Provisional
Probab=21.72 E-value=59 Score=34.93 Aligned_cols=29 Identities=21% Similarity=0.349 Sum_probs=20.0
Q ss_pred eeeeeeccccceEEeecccceeEeccCCCCCcc
Q psy7583 391 YRIHVCNFCGLIAIANMRNNTFECKGCKNKTQI 423 (451)
Q Consensus 391 ~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~ 423 (451)
...|+|.+||.-.. +-.+.|+.|+.=..+
T Consensus 5 ~~~y~C~~Cg~~~~----~~~g~Cp~C~~w~t~ 33 (446)
T PRK11823 5 KTAYVCQECGAESP----KWLGRCPECGAWNTL 33 (446)
T ss_pred CCeEECCcCCCCCc----ccCeeCcCCCCccce
Confidence 35699999997532 235689999864444
No 101
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.57 E-value=64 Score=32.27 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=18.8
Q ss_pred eeccccceEEee--cccceeEeccCCCC
Q psy7583 395 VCNFCGLIAIAN--MRNNTFECKGCKNK 420 (451)
Q Consensus 395 vC~~CG~~~~~~--~~~~~~~C~~C~~~ 420 (451)
-|..||...... ....+|+|+.|...
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 599999876532 23468899999853
No 102
>KOG0703|consensus
Probab=20.99 E-value=75 Score=32.29 Aligned_cols=61 Identities=30% Similarity=0.368 Sum_probs=35.3
Q ss_pred HHHHhhcccCCceeeeeeccccceE--EeecccceeEeccCCC-----CCcc---ceecCchhHHHHHHHHHhCC
Q psy7583 379 FLRERLFEVSDPYRIHVCNFCGLIA--IANMRNNTFECKGCKN-----KTQI---SQVRLPYAAKLLFQELMSMN 443 (451)
Q Consensus 379 ~l~e~l~~~SD~~~~~vC~~CG~~~--~~~~~~~~~~C~~C~~-----~~~~---~~v~iPy~~klL~~EL~sm~ 443 (451)
.|+|.|. .+| ..+|..||... |....-+.|.|..|.. +..| ..|.+=.=..==+++|.+||
T Consensus 15 ~l~~Ll~-~~~---N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~G 85 (287)
T KOG0703|consen 15 RLRELLR-EPD---NKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMG 85 (287)
T ss_pred HHHHHHc-Ccc---cCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHc
Confidence 4556554 455 67899999762 2223347899999974 2222 33444333333456666666
No 103
>PF00799 Gemini_AL1: Geminivirus Rep catalytic domain; InterPro: IPR022690 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome []. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer []. It is found in association with PF08283 from PFAM. ; GO: 0006260 DNA replication; PDB: 1L5I_A 1L2M_A.
Probab=20.90 E-value=37 Score=29.74 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=15.2
Q ss_pred CCccceEeccCCCccceeccccccc
Q psy7583 11 RMDTLAHVLYYPHKPLVTTRSMEYL 35 (451)
Q Consensus 11 R~D~~~~~L~yPQ~Plv~T~~~~~~ 35 (451)
|.-++-+.|+|||.||-.-.+.+.+
T Consensus 2 ri~akn~FLTYpqC~l~ke~~l~~L 26 (114)
T PF00799_consen 2 RIQAKNYFLTYPQCSLTKEEALEQL 26 (114)
T ss_dssp --EEEEEEEEETT----HHHHHHHH
T ss_pred ccccceeeeEccCCCCCHHHHHHHH
Confidence 5667889999999999877666654
No 104
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=20.46 E-value=55 Score=27.52 Aligned_cols=24 Identities=25% Similarity=0.789 Sum_probs=18.2
Q ss_pred eeccccceEEeecccceeEeccCCCC
Q psy7583 395 VCNFCGLIAIANMRNNTFECKGCKNK 420 (451)
Q Consensus 395 vC~~CG~~~~~~~~~~~~~C~~C~~~ 420 (451)
.|+.||.++.. ..+.+.|+.|+..
T Consensus 2 fC~~Cg~~l~~--~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTP--KNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCccccc--CCCeEECcCCCCc
Confidence 49999998864 3457889999854
No 105
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.08 E-value=82 Score=27.48 Aligned_cols=28 Identities=18% Similarity=0.586 Sum_probs=20.2
Q ss_pred eeeccccceEEeec--ccceeEeccCCCCC
Q psy7583 394 HVCNFCGLIAIANM--RNNTFECKGCKNKT 421 (451)
Q Consensus 394 ~vC~~CG~~~~~~~--~~~~~~C~~C~~~~ 421 (451)
..|.+||++++... ....+.|+.|+...
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 46999999988632 34578899998543
No 106
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.00 E-value=72 Score=32.05 Aligned_cols=24 Identities=25% Similarity=0.499 Sum_probs=17.4
Q ss_pred eeccccceEEee--cccceeEeccCC
Q psy7583 395 VCNFCGLIAIAN--MRNNTFECKGCK 418 (451)
Q Consensus 395 vC~~CG~~~~~~--~~~~~~~C~~C~ 418 (451)
-|..||...... ....+|+|+.|.
T Consensus 256 pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCeeEEEEECCCccEECCCCc
Confidence 599999876432 234678899996
Done!