Query psy16768
Match_columns 154
No_of_seqs 123 out of 889
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 21:31:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16768.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16768hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 5.4E-38 1.2E-42 274.6 9.7 117 3-120 221-366 (367)
2 cd02584 RNAP_II_Rpb1_C Largest 100.0 1.3E-37 2.9E-42 275.3 9.8 117 4-121 265-410 (410)
3 cd02736 RNAP_III_Rpc1_C Larges 100.0 2.5E-37 5.3E-42 264.3 10.6 111 5-116 161-300 (300)
4 cd02735 RNAP_I_Rpa1_C Largest 100.0 3E-37 6.5E-42 264.5 10.4 115 5-119 167-309 (309)
5 cd06528 RNAP_A'' A'' subunit o 100.0 3.9E-37 8.4E-42 268.8 9.8 118 3-121 216-362 (363)
6 PRK04309 DNA-directed RNA poly 100.0 4.3E-37 9.2E-42 270.1 9.5 120 3-123 233-381 (383)
7 PRK14897 unknown domain/DNA-di 100.0 5.4E-37 1.2E-41 276.6 9.6 119 5-124 359-506 (509)
8 cd02737 RNAP_IV_NRPD1_C Larges 100.0 3.6E-35 7.8E-40 257.8 10.3 116 3-119 216-380 (381)
9 PRK14898 DNA-directed RNA poly 100.0 6.5E-35 1.4E-39 276.4 9.9 120 5-125 705-853 (858)
10 KOG0262|consensus 100.0 9.9E-34 2.2E-38 271.7 7.4 117 8-124 1494-1638(1640)
11 PRK14977 bifunctional DNA-dire 100.0 7.6E-33 1.6E-37 270.8 9.6 117 5-122 1166-1317(1321)
12 KOG0261|consensus 100.0 9.7E-29 2.1E-33 233.7 6.9 119 5-124 1217-1364(1386)
13 cd00630 RNAP_largest_subunit_C 99.9 4E-28 8.7E-33 191.4 7.0 83 33-115 47-158 (158)
14 KOG0260|consensus 99.9 1.5E-25 3.3E-30 215.1 9.0 129 4-133 1274-1431(1605)
15 PF04998 RNA_pol_Rpb1_5: RNA p 99.9 1.8E-23 3.9E-28 169.6 5.9 90 3-92 177-270 (277)
16 cd02655 RNAP_beta'_C Largest s 99.9 3.7E-23 8.1E-28 169.1 7.3 82 34-115 54-204 (204)
17 PRK00566 DNA-directed RNA poly 99.7 1.8E-17 4E-22 161.2 6.1 85 33-117 988-1139(1156)
18 TIGR02386 rpoC_TIGR DNA-direct 99.7 4.5E-17 9.7E-22 158.4 6.9 84 33-116 986-1136(1140)
19 PRK14844 bifunctional DNA-dire 99.6 1.9E-16 4E-21 161.9 4.0 83 33-115 2635-2784(2836)
20 PRK14906 DNA-directed RNA poly 99.5 6.3E-15 1.4E-19 145.3 6.9 84 33-116 1087-1237(1460)
21 PRK02597 rpoC2 DNA-directed RN 99.5 6.9E-15 1.5E-19 144.7 6.2 84 33-116 1058-1224(1331)
22 TIGR02388 rpoC2_cyan DNA-direc 99.5 1.2E-14 2.6E-19 142.1 6.2 84 33-116 1057-1223(1227)
23 CHL00117 rpoC2 RNA polymerase 99.5 1.5E-14 3.2E-19 143.0 6.3 81 43-123 1181-1325(1364)
24 PRK09603 bifunctional DNA-dire 99.4 8.6E-14 1.9E-18 143.1 5.7 83 33-115 2724-2873(2890)
25 COG0086 RpoC DNA-directed RNA 98.4 3.7E-08 8.1E-13 94.3 -1.6 117 5-122 601-746 (808)
26 COG3688 Predicted RNA-binding 75.2 4 8.8E-05 33.1 3.6 44 8-64 5-48 (173)
27 PF08546 ApbA_C: Ketopantoate 53.6 21 0.00045 25.7 3.6 56 35-90 26-82 (125)
28 PF14769 CLAMP: Flagellar C1a 47.4 27 0.00057 25.1 3.3 36 47-82 36-79 (101)
29 PF12335 SBF2: Myotubularin pr 40.0 68 0.0015 26.9 5.1 46 36-81 46-91 (225)
30 PF04998 RNA_pol_Rpb1_5: RNA p 37.3 13 0.00028 29.9 0.4 49 35-83 169-217 (277)
31 PF13421 Band_7_1: SPFH domain 35.6 57 0.0012 26.7 3.9 44 47-90 136-184 (211)
32 PF01257 2Fe-2S_thioredx: Thio 29.9 56 0.0012 24.9 2.8 44 36-82 1-44 (145)
33 PRK07539 NADH dehydrogenase su 29.3 1.2E+02 0.0026 23.4 4.7 44 35-82 9-53 (154)
34 KOG1914|consensus 28.9 63 0.0014 31.1 3.4 57 18-82 356-412 (656)
35 TIGR01958 nuoE_fam NADH-quinon 27.1 83 0.0018 24.1 3.3 43 36-82 2-47 (148)
36 TIGR00745 apbA_panE 2-dehydrop 26.8 77 0.0017 25.6 3.3 56 46-101 203-264 (293)
37 CHL00077 rps18 ribosomal prote 24.9 37 0.00081 24.7 1.0 20 64-83 25-44 (86)
38 PF13096 CENP-P: CENP-A-nucleo 22.8 45 0.00098 27.3 1.2 22 32-53 156-177 (177)
39 PTZ00373 60S Acidic ribosomal 22.4 1.1E+02 0.0023 23.2 3.1 29 54-82 23-51 (112)
40 cd05833 Ribosomal_P2 Ribosomal 21.8 1.1E+02 0.0024 22.8 3.1 27 54-80 21-47 (109)
41 PF05991 NYN_YacP: YacP-like N 21.6 70 0.0015 25.0 2.0 40 9-61 1-40 (166)
42 PF06505 XylR_N: Activator of 21.4 1E+02 0.0022 22.8 2.7 17 37-53 35-51 (103)
43 PF10598 RRM_4: RNA recognitio 21.2 48 0.001 24.5 0.9 17 75-91 20-47 (93)
44 COG5107 RNA14 Pre-mRNA 3'-end 20.8 79 0.0017 30.2 2.4 48 28-75 396-443 (660)
45 PF01084 Ribosomal_S18: Riboso 20.5 28 0.0006 22.9 -0.4 24 64-87 4-29 (54)
46 PF09419 PGP_phosphatase: Mito 20.4 14 0.0003 29.6 -2.2 54 36-89 98-158 (168)
47 PRK07571 bidirectional hydroge 20.3 2.4E+02 0.0052 22.5 4.9 44 35-82 23-67 (169)
48 cd05831 Ribosomal_P1 Ribosomal 20.2 1.2E+02 0.0027 22.2 3.0 27 54-80 21-47 (103)
No 1
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=5.4e-38 Score=274.56 Aligned_cols=117 Identities=28% Similarity=0.353 Sum_probs=111.6
Q ss_pred CCCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 3 ~~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
++++|+|+|+|+||+++|.++ +||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++
T Consensus 221 ~~~~~~l~teG~nl~~v~~~~-~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~ 299 (367)
T TIGR02389 221 EGDEYVIYTEGSNLKEVLKLE-GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWD 299 (367)
T ss_pred CCCeEEEEEeccCHHHHHcCC-CCccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCC
Confidence 467899999999999999995 9999999999999999999999999999999999999999999999999999999999
Q ss_pred c----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhh
Q psy16768 83 E----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVK 120 (154)
Q Consensus 83 G----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~ 120 (154)
| +||+|++++. |+.|+|+|||+||++| |+|||+|+++.
T Consensus 300 G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~ 366 (367)
T TIGR02389 300 GEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVM 366 (367)
T ss_pred ceEEeccccccccCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEee
Confidence 9 9999997532 9999999999999999 99999999875
No 2
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=100.00 E-value=1.3e-37 Score=275.29 Aligned_cols=117 Identities=24% Similarity=0.310 Sum_probs=111.4
Q ss_pred CCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc
Q psy16768 4 NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE 83 (154)
Q Consensus 4 ~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G 83 (154)
+++|+|+|+|+||+++|+++ +||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|
T Consensus 265 ~~~~~l~teG~nl~~v~~~~-~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G 343 (410)
T cd02584 265 REEWVLETDGVNLREVLSHP-GVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRG 343 (410)
T ss_pred CcceEEEecCcCHHHHhCCC-CCccccCEeCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhhce
Confidence 46899999999999999995 99999999999999999999999999999999999999999999999999999999999
Q ss_pred ----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhh
Q psy16768 84 ----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKK 121 (154)
Q Consensus 84 ----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~ 121 (154)
+||+||++.. |+.|+|+|||+||++| |+|||+|+++.|
T Consensus 344 ~~~~i~R~Gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~f~l~~d 410 (410)
T cd02584 344 HLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLLLD 410 (410)
T ss_pred EEeeEeeeeeeccCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheeecCccccccceEEEEeC
Confidence 9999997532 9999999999999999 999999998864
No 3
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=2.5e-37 Score=264.33 Aligned_cols=111 Identities=23% Similarity=0.282 Sum_probs=106.6
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE- 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G- 83 (154)
++|+|+|+|+||+++|.+ ++||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|
T Consensus 161 ~~~~l~teG~nl~~v~~~-~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~ 239 (300)
T cd02736 161 GKYKLLVEGYGLRAVMNT-PGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGE 239 (300)
T ss_pred CcEEEEEecccHHHHhcC-CcEeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCc
Confidence 689999999999999999 599999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cchhhhccc--c--------------------ccccccCCcccceeec---CCCCCch
Q psy16768 84 ---FDLIIMVSK--S--------------------WMLDEVKSTTARSVTP---ACEPNSH 116 (154)
Q Consensus 84 ---~~R~Gm~~~--~--------------------g~~D~l~svSa~Ii~G---~~GTG~~ 116 (154)
+||+|+++. + |+.|+|+|||++|++| |+|||+|
T Consensus 240 ~~~itR~gi~~~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 240 VLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred eeeeecccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcCCCcHHHeeeCCCcCCCCCCC
Confidence 999999742 1 9999999999999999 9999986
No 4
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=3e-37 Score=264.47 Aligned_cols=115 Identities=45% Similarity=0.709 Sum_probs=109.4
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE- 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G- 83 (154)
.+|.|+|+|+||+++|.++++||++|++||||++++++|||||||++|++|+++||+.||++||+|||+||||+||++|
T Consensus 167 ~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~ 246 (309)
T cd02735 167 TKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGG 246 (309)
T ss_pred eEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCc
Confidence 3799999999999999997799999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cchhhhcccc---------------------ccccccCCcccceeec---CCCCCchhhh
Q psy16768 84 ---FDLIIMVSKS---------------------WMLDEVKSTTARSVTP---ACEPNSHHDV 119 (154)
Q Consensus 84 ---~~R~Gm~~~~---------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~ 119 (154)
+||+||+.+. |+.|+|+|+|+||++| |+|||+|+++
T Consensus 247 ~~~~nr~gi~~~~S~l~~asFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 247 YRPFNRIGMESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred EeecchhheccCCCHHHhhhhhhHHHHHHHHhhcCCCCCCCChHHheeeCCccCccceeEEeC
Confidence 9999995432 9999999999999999 9999998874
No 5
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=3.9e-37 Score=268.80 Aligned_cols=118 Identities=25% Similarity=0.329 Sum_probs=111.9
Q ss_pred CCCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 3 ~~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
++++|+|+|+|+||+++|.++ +||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++
T Consensus 216 ~~~~~~l~teG~nl~~v~~~~-~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~ 294 (363)
T cd06528 216 EEDEYVIYTEGSNLKAVLKVE-GVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYD 294 (363)
T ss_pred CCceEEEEecCcCHHHHhcCC-CCcccccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccC
Confidence 356899999999999999995 9999999999999999999999999999999999999999999999999999999999
Q ss_pred c----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhh
Q psy16768 83 E----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKK 121 (154)
Q Consensus 83 G----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~ 121 (154)
| +||+|++++. |+.|+|.|||++|++| |+|||+|+++.+
T Consensus 295 G~~~~i~R~gi~~~~~S~L~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d 362 (363)
T cd06528 295 GEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMD 362 (363)
T ss_pred CceecccchhhcCCCCChhhhCchhhHHHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEec
Confidence 9 9999996532 9999999999999999 999999999865
No 6
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=4.3e-37 Score=270.09 Aligned_cols=120 Identities=27% Similarity=0.335 Sum_probs=113.9
Q ss_pred CCCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 3 ~~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
++++|+|+|+|+||+++|.+ ++||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++
T Consensus 233 ~~~~~~l~teG~nl~~v~~~-~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~ 311 (383)
T PRK04309 233 EGDEYVIYTEGSNLKEVLKV-EGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWD 311 (383)
T ss_pred CCCeEEEEEcccCHHHHhcC-CCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccC
Confidence 35789999999999999999 59999999999999999999999999999999999999999999999999999999999
Q ss_pred c----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhh
Q psy16768 83 E----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIE 123 (154)
Q Consensus 83 G----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~ 123 (154)
| +||+|+++.. |+.|+|+|+|++|++| |+|||+|+++.+.+
T Consensus 312 G~~~~i~R~Gi~~~~~S~l~~aSFE~T~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~ 381 (383)
T PRK04309 312 GEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPP 381 (383)
T ss_pred ceEEeeechhhcCCCCCHHHhCchhhHHHHHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCC
Confidence 9 9999996532 9999999999999999 99999999998765
No 7
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=5.4e-37 Score=276.58 Aligned_cols=119 Identities=27% Similarity=0.324 Sum_probs=112.8
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE- 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G- 83 (154)
++|+|+|+|+||+++|++ ++||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|
T Consensus 359 ~~~~L~TeG~NL~~vl~~-~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~ 437 (509)
T PRK14897 359 RRWVIYTQGSNLKDVLEI-DEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGS 437 (509)
T ss_pred ceeEEEeeccCHHHHhcC-CCcccccCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCc
Confidence 469999999999999999 599999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhhh
Q psy16768 84 ---FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIEF 124 (154)
Q Consensus 84 ---~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~~ 124 (154)
+||+||+... |+.|+|.|||+||++| |+|||+|+++.+..+
T Consensus 438 v~~i~R~Gi~~~~~SpL~rASFE~T~~~L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~~ 506 (509)
T PRK14897 438 VKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRK 506 (509)
T ss_pred ccccccccccccCCCHHHhcchHhHHHHHHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCCC
Confidence 9999996532 9999999999999999 999999999987653
No 8
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=100.00 E-value=3.6e-35 Score=257.82 Aligned_cols=116 Identities=22% Similarity=0.247 Sum_probs=109.4
Q ss_pred CCCeEEEEEe---------cCChHHHhc-----cCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccc
Q psy16768 3 TNGKHLLKTD---------GINVNYISQ-----YRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVD 68 (154)
Q Consensus 3 ~~~~~~l~te---------G~nl~~~~~-----~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd 68 (154)
..+||+|+|+ |.+++.++. + ++||++|++||||++|+++|||||||+.|++|+++||+.||++||
T Consensus 216 ~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~-~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G~~Vd 294 (381)
T cd02737 216 SRGELVLEVTVEESCKKTRGNAWNVVMDACIPVM-DLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVL 294 (381)
T ss_pred ccceEEEEEEeccccccccchhHHHHHHhhhccc-ccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCccc
Confidence 4679999988 999999995 6 699999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHhhhc----cchhhhccc-------c--------------------ccccccCCcccceeec---CCCCC
Q psy16768 69 PRHLSLVADYMTHSE----FDLIIMVSK-------S--------------------WMLDEVKSTTARSVTP---ACEPN 114 (154)
Q Consensus 69 ~rHi~LIaD~MT~~G----~~R~Gm~~~-------~--------------------g~~D~l~svSa~Ii~G---~~GTG 114 (154)
+|||.||||+||++| |||+||++. + |+.|+|+|||++|++| ++|||
T Consensus 295 ~rHL~LlAD~MT~~G~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG 374 (381)
T cd02737 295 REHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTG 374 (381)
T ss_pred HHHHHHHHHHhccCCceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCC
Confidence 999999999999999 999999942 1 9999999999999999 99999
Q ss_pred c-hhhh
Q psy16768 115 S-HHDV 119 (154)
Q Consensus 115 ~-~~~~ 119 (154)
. |+++
T Consensus 375 ~~fdll 380 (381)
T cd02737 375 SKFEIL 380 (381)
T ss_pred cceeee
Confidence 7 8876
No 9
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=6.5e-35 Score=276.41 Aligned_cols=120 Identities=27% Similarity=0.303 Sum_probs=114.4
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE- 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G- 83 (154)
++|+|+|+|+||+++|.++ +||++|++||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|
T Consensus 705 ~~~~l~teG~nl~~~~~~~-~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~ 783 (858)
T PRK14898 705 EEYVLYTQGSNLREVFKIE-GVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGE 783 (858)
T ss_pred ceEEEEecCcCHHHHhcCC-CCcccccccCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCc
Confidence 5899999999999999995 99999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhhhh
Q psy16768 84 ---FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIEFK 125 (154)
Q Consensus 84 ---~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~~~ 125 (154)
+||+||+.+. |+.|+|+|||+||++| |+|||+|+++.+.++.
T Consensus 784 ~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~~~l~~~~~~~ 853 (858)
T PRK14898 784 VKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDREYE 853 (858)
T ss_pred EEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCCchHHeeeCCccCCcCceEEEEecCccc
Confidence 9999996532 9999999999999999 9999999999988753
No 10
>KOG0262|consensus
Probab=100.00 E-value=9.9e-34 Score=271.66 Aligned_cols=117 Identities=46% Similarity=0.679 Sum_probs=113.2
Q ss_pred EEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc----
Q psy16768 8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE---- 83 (154)
Q Consensus 8 ~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G---- 83 (154)
+++|+|+||.++|.+.+.+|.+++|||||++|+++|||||||++|++||+.||+.|||+||+|||+|||||||+.|
T Consensus 1494 ~l~TeGVnl~a~~~~~d~LDv~~lySNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYMTf~G~y~p 1573 (1640)
T KOG0262|consen 1494 VLLTEGVNLPALFDHADILDVNRLYSNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGYQP 1573 (1640)
T ss_pred eehhcCccHHHHHHHHhhhhhhhhccchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHHhhcccccc
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhcccc---------------------ccccccCCcccceeec---CCCCCchhhhhhhhh
Q psy16768 84 FDLIIMVSKS---------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIEF 124 (154)
Q Consensus 84 ~~R~Gm~~~~---------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~~ 124 (154)
|||+||..++ |+.|.|++||||+++| .+|||+|+++.+.++
T Consensus 1574 fnR~Gm~~ssSP~qkMsFETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~~ 1638 (1640)
T KOG0262|consen 1574 FNRMGMESSSSPLQKMSFETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVDF 1638 (1640)
T ss_pred ccccccccCCChhHhhhHHHHHHHHHHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCCC
Confidence 9999999765 9999999999999999 779999999988764
No 11
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=99.98 E-value=7.6e-33 Score=270.82 Aligned_cols=117 Identities=22% Similarity=0.315 Sum_probs=111.9
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE- 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G- 83 (154)
++|+|+|+|+||+++|.++ +||+.||+||||+||+++|||||||++|++|+++||+.||++||+|||+||||+||++|
T Consensus 1166 ~e~~l~teG~nl~~vl~~~-~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei~~v~~~~G~~V~~rHi~LlaD~MT~~G~ 1244 (1321)
T PRK14977 1166 DEWIIQTSGSNLAAVLEMK-CIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGT 1244 (1321)
T ss_pred eeEEEEecCcCHHHHhCCC-CCcccccEECCHHHHHHhhhHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHccCce
Confidence 5899999999999999995 99999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cc------hhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhh
Q psy16768 84 ---FD------LIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKI 122 (154)
Q Consensus 84 ---~~------R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~ 122 (154)
++ |+||++.. |+.|.|+||||+||+| |+|||+|+++.+.
T Consensus 1245 ~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvsenii~G~~~~~GTG~~~Ll~~~ 1317 (1321)
T PRK14977 1245 IEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDF 1317 (1321)
T ss_pred EEeccccccccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChHHhhhcCCCccCccceEEEEecc
Confidence 99 99998742 9999999999999999 9999999988764
No 12
>KOG0261|consensus
Probab=99.95 E-value=9.7e-29 Score=233.70 Aligned_cols=119 Identities=19% Similarity=0.243 Sum_probs=113.1
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE- 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G- 83 (154)
+.|.|.+||.+|+++++. ++|+..||.||++.||.++|||||||..||+||..+|..+|++||+||++|+||.||++|
T Consensus 1217 ~~y~L~vEG~gLr~Vm~t-~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGE 1295 (1386)
T KOG0261|consen 1217 GLYKLLVEGTGLRAVMNT-DGVKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGE 1295 (1386)
T ss_pred CceEEEEeccchHHHhcc-CCccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCcccCHHHHHHHHHHhhhcce
Confidence 449999999999999999 699999999999999999999999999999999999999999999999999999999999
Q ss_pred ---cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhhh
Q psy16768 84 ---FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIEF 124 (154)
Q Consensus 84 ---~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~~ 124 (154)
++|+|+.+.. +++|.+.|||+|||+| .+|||.|+++..-+.
T Consensus 1296 VlGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~fkl~~~~~~ 1364 (1386)
T KOG0261|consen 1296 VLGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGIFKLLQRTDD 1364 (1386)
T ss_pred eeeeeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhheecccceeccccHHHHHHhcCC
Confidence 9999988743 9999999999999999 779999999988764
No 13
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.95 E-value=4e-28 Score=191.43 Aligned_cols=83 Identities=34% Similarity=0.422 Sum_probs=78.1
Q ss_pred eccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc----cchhhhcccc---------------
Q psy16768 33 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE----FDLIIMVSKS--------------- 93 (154)
Q Consensus 33 sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G----~~R~Gm~~~~--------------- 93 (154)
+-||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++| +||+||+.+.
T Consensus 47 ~~dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~ 126 (158)
T cd00630 47 AASIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKH 126 (158)
T ss_pred cccHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHH
Confidence 349999999999999999999999999999999999999999999999999 9999995321
Q ss_pred -------ccccccCCcccceeec---CCCCCc
Q psy16768 94 -------WMLDEVKSTTARSVTP---ACEPNS 115 (154)
Q Consensus 94 -------g~~D~l~svSa~Ii~G---~~GTG~ 115 (154)
++.|+|+|+|++|++| |+|||+
T Consensus 127 L~~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 127 LLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred HHHHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 9999999999999999 899995
No 14
>KOG0260|consensus
Probab=99.92 E-value=1.5e-25 Score=215.12 Aligned_cols=129 Identities=23% Similarity=0.266 Sum_probs=123.3
Q ss_pred CCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc
Q psy16768 4 NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE 83 (154)
Q Consensus 4 ~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G 83 (154)
-++|.|+|+|+||.+++..| .||..|++|||+.++.+++||||+|.++++|+..|....|.+||+||+.|++|.||.+|
T Consensus 1274 ~~ew~LeTdg~~l~~v~s~~-~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g 1352 (1605)
T KOG0260|consen 1274 VDEWDLETDGVNLRRVLSEP-DVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARG 1352 (1605)
T ss_pred cceeEEecCchhHHhhhccC-CCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhccc
Confidence 37999999999999999996 89999999999999999999999999999999999999999999999999999999999
Q ss_pred ----cchhhhcccc----------------------ccccccCCcccceeec---CCCCCchhhhhhhhhhcccccccc
Q psy16768 84 ----FDLIIMVSKS----------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIEFKKQNKILPL 133 (154)
Q Consensus 84 ----~~R~Gm~~~~----------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~~~~~~~~~~~ 133 (154)
++|||+++.. ++.|.++|++++|++| |+|||.|+++.+.|.++..+..|.
T Consensus 1353 ~lm~itRhg~nr~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e~l~~~~~~~~ 1431 (1605)
T KOG0260|consen 1353 HLMAITRHGINRQDTGALMRCSFEETVDILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAEKLKKGIEIPM 1431 (1605)
T ss_pred ceeeeeccccchhhccccccccHHHHHHHHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHHhhhccCccCC
Confidence 9999998743 9999999999999999 999999999999999998888775
No 15
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 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). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=99.88 E-value=1.8e-23 Score=169.58 Aligned_cols=90 Identities=43% Similarity=0.592 Sum_probs=85.6
Q ss_pred CCCeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 3 ~~~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
.+.+|.++++|+||..+|..++.+|++++++|||++|+++|||||||+.|++|++.|+..+|+.||+|||.|+||+||++
T Consensus 177 ~~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~ 256 (277)
T PF04998_consen 177 KSKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYK 256 (277)
T ss_dssp CCCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCC
T ss_pred hhHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeee
Confidence 46789999999999999999866999999999999999999999999999999999999999999999999999999999
Q ss_pred c----cchhhhccc
Q psy16768 83 E----FDLIIMVSK 92 (154)
Q Consensus 83 G----~~R~Gm~~~ 92 (154)
| |||+||+++
T Consensus 257 g~~~gitR~gl~~~ 270 (277)
T PF04998_consen 257 GVLLGITRHGLNSN 270 (277)
T ss_dssp SS---CCTTTTSSS
T ss_pred eEEEEEEHHHhccC
Confidence 9 999999854
No 16
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.88 E-value=3.7e-23 Score=169.05 Aligned_cols=82 Identities=15% Similarity=0.280 Sum_probs=73.6
Q ss_pred ccHHHHHHhh--CHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc----------------------------
Q psy16768 34 NDIHYMASTY--GIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE---------------------------- 83 (154)
Q Consensus 34 NdI~~i~~~l--GIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G---------------------------- 83 (154)
||++++++++ ||||+|++|++|+++||+.||++||+|||+|||||||+++
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 9999999999 9999999999999999999999999999999999999992
Q ss_pred ----------------cchhhhcccc--------------------ccccccCCcccceeec---CCCCCc
Q psy16768 84 ----------------FDLIIMVSKS--------------------WMLDEVKSTTARSVTP---ACEPNS 115 (154)
Q Consensus 84 ----------------~~R~Gm~~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~ 115 (154)
+||+++...+ |+.|.|+|+++|||+| |+|||+
T Consensus 134 ~~~~~~~~~y~p~llGItk~~l~~~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 134 LLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred HhCCCCcccccceeeeeeeccccCCCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 3333333222 9999999999999999 999995
No 17
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.69 E-value=1.8e-17 Score=161.23 Aligned_cols=85 Identities=15% Similarity=0.318 Sum_probs=75.3
Q ss_pred eccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-----------------------------
Q psy16768 33 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE----------------------------- 83 (154)
Q Consensus 33 sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G----------------------------- 83 (154)
+-|++++++++|+||+|++|++|+|+||+.||++||+|||++|+||||.++
T Consensus 988 ~~~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~~~g~~v~~~~~~~~n~~~~ 1067 (1156)
T PRK00566 988 SIDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLI 1067 (1156)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCCCCCceeeHHHHHHHHHHHH
Confidence 347999999999999999999999999999999999999999999999852
Q ss_pred ---------------cchhhhcccc--------------------ccccccCCcccceeec---CCCCCchh
Q psy16768 84 ---------------FDLIIMVSKS--------------------WMLDEVKSTTARSVTP---ACEPNSHH 117 (154)
Q Consensus 84 ---------------~~R~Gm~~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~~~ 117 (154)
+||.+++..+ |++|+|.|++++||+| |+|||+..
T Consensus 1068 ~~g~~~~~~~~~llGItka~l~t~SflsaASFQeTtkvLt~AAi~gk~D~L~GlkENVIiG~liPaGTG~~~ 1139 (1156)
T PRK00566 1068 AEGKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLAR 1139 (1156)
T ss_pred HCCCCCCcccceeeeeeecccccCcccccccccchHHHHHHHHhcCCCCcCCCcccceEecCcccCCCCcch
Confidence 5555554322 9999999999999999 99999853
No 18
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=99.68 E-value=4.5e-17 Score=158.42 Aligned_cols=84 Identities=18% Similarity=0.318 Sum_probs=74.2
Q ss_pred eccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc---------------cchhhhc-------
Q psy16768 33 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE---------------FDLIIMV------- 90 (154)
Q Consensus 33 sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G---------------~~R~Gm~------- 90 (154)
+-|++++++++||||++++|++|+|+||+.||++||+|||++|++|||+++ ++|+.+.
T Consensus 986 ~~~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~l~g~~v~~~~~~~~n~~~~ 1065 (1140)
T TIGR02386 986 SIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLL 1065 (1140)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCcCCCCCCeeeHHHHHHHHHHHH
Confidence 457999999999999999999999999999999999999999999999994 4444432
Q ss_pred ----------------------ccc--------------------ccccccCCcccceeec---CCCCCch
Q psy16768 91 ----------------------SKS--------------------WMLDEVKSTTARSVTP---ACEPNSH 116 (154)
Q Consensus 91 ----------------------~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~~ 116 (154)
..+ |++|+|.|++++||+| |+|||+.
T Consensus 1066 ~~g~~~~~~~~~llGitkasl~t~SflsaASFqeTtkvLt~Aai~gk~D~L~GlkENVIiG~liPaGTG~~ 1136 (1140)
T TIGR02386 1066 EQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLK 1136 (1140)
T ss_pred hCCCCCccceeeeeeeeehhccCCCcccccchhhHHHHHHHHHhcCCCCCCCCcccceEecCcccCCCCcc
Confidence 111 9999999999999999 9999974
No 19
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=99.62 E-value=1.9e-16 Score=161.90 Aligned_cols=83 Identities=18% Similarity=0.316 Sum_probs=73.9
Q ss_pred eccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh------------------------------
Q psy16768 33 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS------------------------------ 82 (154)
Q Consensus 33 sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~------------------------------ 82 (154)
+.|++++++++|+||++++|++|+|+||+.||+.||+|||++|++|||++
T Consensus 2635 ~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt~~l~Ge~v~~~~~~~~n~~~~ 2714 (2836)
T PRK14844 2635 DPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMS 2714 (2836)
T ss_pred CCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCcccCCCceecHHHHHHHHHHHH
Confidence 46799999999999999999999999999999999999999999999987
Q ss_pred --------------ccchhhhcccc--------------------ccccccCCcccceeec---CCCCCc
Q psy16768 83 --------------EFDLIIMVSKS--------------------WMLDEVKSTTARSVTP---ACEPNS 115 (154)
Q Consensus 83 --------------G~~R~Gm~~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~ 115 (154)
|+||+.++..+ |++|+|.|++++||+| |+|||+
T Consensus 2715 ~~g~~pa~~~pvllGITkasL~t~SflSaASFQeTtkVLt~AAi~Gk~D~L~GlKENVIiG~lIPaGTG~ 2784 (2836)
T PRK14844 2715 NSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784 (2836)
T ss_pred hcCCCCceeeeeeeceeeccccCCChhhcCCcccchHHHHHHHhcCCCCcCCCcccceEecCcccCCcCc
Confidence 24444443322 9999999999999999 999996
No 20
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=99.55 E-value=6.3e-15 Score=145.28 Aligned_cols=84 Identities=13% Similarity=0.239 Sum_probs=73.0
Q ss_pred eccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc---------------cchhh---------
Q psy16768 33 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE---------------FDLII--------- 88 (154)
Q Consensus 33 sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G---------------~~R~G--------- 88 (154)
+-|+++++++.|+||++++|++|||+||+.||+.||+|||++|+.||+++. ++|.-
T Consensus 1087 ~~~p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d~Gdt~fl~Ge~vd~~~~~~~n~~~~ 1166 (1460)
T PRK14906 1087 SVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLI 1166 (1460)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEecCCCcCCCCCCeeeHHHHHHHHHHHH
Confidence 457999999999999999999999999999999999999999999999983 23322
Q ss_pred --------------------hcccc--------------------ccccccCCcccceeec---CCCCCch
Q psy16768 89 --------------------MVSKS--------------------WMLDEVKSTTARSVTP---ACEPNSH 116 (154)
Q Consensus 89 --------------------m~~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~~ 116 (154)
++..+ |++|.|.|+.++||+| |+|||+.
T Consensus 1167 ~~g~~pa~~~p~llGITKasL~t~SflSaASFQeTtrVLt~AAi~gk~D~L~GLKENVIiG~lIPAGTG~~ 1237 (1460)
T PRK14906 1167 LEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLS 1237 (1460)
T ss_pred HcCCCCceeeeEEeeeeecccccccccccccccchHHHHHHHHhcCCCCcCCCCccceEecceecCCCCcc
Confidence 21111 9999999999999999 9999984
No 21
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.54 E-value=6.9e-15 Score=144.74 Aligned_cols=84 Identities=14% Similarity=0.238 Sum_probs=73.5
Q ss_pred eccHHHHHHh----------------hCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-------------
Q psy16768 33 VNDIHYMAST----------------YGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE------------- 83 (154)
Q Consensus 33 sNdI~~i~~~----------------lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G------------- 83 (154)
+.++|+++++ .|+||+|..+++|+|+||+.||+.||+|||++|+|+||.++
T Consensus 1058 ~~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvrqMt~kV~i~d~Gdt~~lpG 1137 (1331)
T PRK02597 1058 PINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPG 1137 (1331)
T ss_pred CCCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHHHHhCcEEEeeCCCcccCCc
Confidence 3788999998 89999999999999999999999999999999999999992
Q ss_pred ----------cc------h----------hhhcccc-------------------------ccccccCCcccceeec---
Q psy16768 84 ----------FD------L----------IIMVSKS-------------------------WMLDEVKSTTARSVTP--- 109 (154)
Q Consensus 84 ----------~~------R----------~Gm~~~~-------------------------g~~D~l~svSa~Ii~G--- 109 (154)
+| + .|+.+.+ |+.|.|+|++++||+|
T Consensus 1138 eli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl~T~sfis~aSFqeT~rvL~~AAi~g~~D~l~GlkENVI~G~li 1217 (1331)
T PRK02597 1138 ELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLI 1217 (1331)
T ss_pred ceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeeccccCChhhhccHHHHHHHHHHHHHcCCCcccCCchhheeecCcc
Confidence 11 1 3333311 9999999999999999
Q ss_pred CCCCCch
Q psy16768 110 ACEPNSH 116 (154)
Q Consensus 110 ~~GTG~~ 116 (154)
|+|||++
T Consensus 1218 P~GTG~~ 1224 (1331)
T PRK02597 1218 PAGTGFS 1224 (1331)
T ss_pred ccCcCch
Confidence 9999996
No 22
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=99.52 E-value=1.2e-14 Score=142.12 Aligned_cols=84 Identities=14% Similarity=0.251 Sum_probs=72.2
Q ss_pred eccHHHHHHh----------------hCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh-------------c
Q psy16768 33 VNDIHYMAST----------------YGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS-------------E 83 (154)
Q Consensus 33 sNdI~~i~~~----------------lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~-------------G 83 (154)
+.++|+++++ +|+||+|..|++|+|+||++||+.|++|||++|+|+||.+ |
T Consensus 1057 ~~~ph~iL~~~~~~~~~~~g~~~aa~~s~~~~q~~lv~eiq~vy~~QGv~I~~kHieiIvrqMtskV~i~~~G~t~~lpG 1136 (1227)
T TIGR02388 1057 PINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPG 1136 (1227)
T ss_pred CCCHHHHHhhhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhcceEeehhhHHHHHHHHhceEEEeeCCCcccCCc
Confidence 4678899888 4999999999999999999999999999999999999999 4
Q ss_pred -------------------------------cchhhhcccc--------------------ccccccCCcccceeec---
Q psy16768 84 -------------------------------FDLIIMVSKS--------------------WMLDEVKSTTARSVTP--- 109 (154)
Q Consensus 84 -------------------------------~~R~Gm~~~~--------------------g~~D~l~svSa~Ii~G--- 109 (154)
+||+.++..+ |+.|.|+|++++||+|
T Consensus 1137 eli~~~~~~~~n~~l~~~~~~~~~y~pvLlGITkasL~t~Sfis~ASFqeTtrvL~~Aai~g~~D~l~glkENvI~G~li 1216 (1227)
T TIGR02388 1137 ELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLI 1216 (1227)
T ss_pred ceeeHHHHHHHHHHHHhcCCCccccceeEeeeeeccccccchhhhccHHHHHHHHHHHHHcCCcccccCchhheeecCcc
Confidence 2233332222 9999999999999999
Q ss_pred CCCCCch
Q psy16768 110 ACEPNSH 116 (154)
Q Consensus 110 ~~GTG~~ 116 (154)
|+|||+.
T Consensus 1217 P~GTG~~ 1223 (1227)
T TIGR02388 1217 PAGTGFS 1223 (1227)
T ss_pred ccCCCcc
Confidence 9999973
No 23
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.51 E-value=1.5e-14 Score=143.00 Aligned_cols=81 Identities=12% Similarity=0.252 Sum_probs=68.4
Q ss_pred hCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh--------------c----------cch------------
Q psy16768 43 YGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS--------------E----------FDL------------ 86 (154)
Q Consensus 43 lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~--------------G----------~~R------------ 86 (154)
+.|||+|..|++|+|+||++||+.|++|||++|+||||.+ | ++|
T Consensus 1181 lS~~~~~~~lv~eiq~vy~~qGv~i~~kHieiivrqmt~kv~i~~~g~~~v~~pge~i~~~~~~~~~~~~~~~~~~~~~l 1260 (1364)
T CHL00117 1181 LSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPIL 1260 (1364)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCcEeehhhhhhhHHHhhCeEEEeecCccCccCCcceeeHHHHHHHhHHhhcCcceeeee
Confidence 3599999999999999999999999999999999999996 2 333
Q ss_pred -----hhhcccc--------------------ccccccCCcccceeec---CCCCCchhhhhhhh
Q psy16768 87 -----IIMVSKS--------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKIE 123 (154)
Q Consensus 87 -----~Gm~~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~~ 123 (154)
++++..+ |+.|.|+|+.++||+| |+|||+........
T Consensus 1261 lGitkasl~t~Sfis~aSFqeT~rvL~~aai~g~~D~l~glkenvi~g~~ip~GTG~~~~~~~~~ 1325 (1364)
T CHL00117 1261 LGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSK 1325 (1364)
T ss_pred eeeeehhccccchhhhcchHHHHHHHHHHHHcCCcccccCchhheeecCcccCCCCchhhhhhhh
Confidence 3333322 9999999999999999 99999976665544
No 24
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=99.44 E-value=8.6e-14 Score=143.12 Aligned_cols=83 Identities=17% Similarity=0.215 Sum_probs=72.8
Q ss_pred eccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc---------------cchh----------
Q psy16768 33 VNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE---------------FDLI---------- 87 (154)
Q Consensus 33 sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G---------------~~R~---------- 87 (154)
+-|+|+++++.|++|..++|++|+|+||+.||+.||+|||++|+.||+++. ++|.
T Consensus 2724 ~~~p~dil~~~g~~~~~~ylv~EVQ~VYr~QGV~InDKHIEvIvrQMl~kV~I~d~GDt~fl~Ge~vd~~~~~~~n~~~~ 2803 (2890)
T PRK09603 2724 VVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVI 2803 (2890)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCEEeccceehhhHhhhheeEEEEcCCCcccCCCceeeHHHHHHHHHHHH
Confidence 347899999999999999999999999999999999999999999999983 3333
Q ss_pred -------------------hhcccc--------------------ccccccCCcccceeec---CCCCCc
Q psy16768 88 -------------------IMVSKS--------------------WMLDEVKSTTARSVTP---ACEPNS 115 (154)
Q Consensus 88 -------------------Gm~~~~--------------------g~~D~l~svSa~Ii~G---~~GTG~ 115 (154)
.++..+ |.+|+|.|..++||+| |+|||+
T Consensus 2804 ~~g~~pa~~~p~LlGITKAsL~t~SfiSAASFQETTkVLteAAi~gk~D~L~glKENVi~G~liPaGTG~ 2873 (2890)
T PRK09603 2804 ALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGM 2873 (2890)
T ss_pred HcCCCCceeeeeeeeeehhhhcccchhhcccccchhHHHHHHHhcCCCCccCCcccceEeeccccccCCc
Confidence 222211 9999999999999999 999998
No 25
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=98.38 E-value=3.7e-08 Score=94.26 Aligned_cols=117 Identities=22% Similarity=0.242 Sum_probs=105.1
Q ss_pred CeEEEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcc-cchhHHHHHHHHHhhhc
Q psy16768 5 GKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIE-VDPRHLSLVADYMTHSE 83 (154)
Q Consensus 5 ~~~~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~-Vd~rHi~LIaD~MT~~G 83 (154)
.+|+..+++.+++.++++ +..|.+++.+||+.++++++++||+++.+.+|+..+...+|.. ++.+|+...++.|+..+
T Consensus 601 ~e~v~~ae~~v~~~i~~~-~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~sq 679 (808)
T COG0086 601 DEIVIEAEGSVLKLILQY-EEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQ 679 (808)
T ss_pred HHHHHHHHHHHHHHHHHh-hcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHHH
Confidence 367888999999999999 5899999999999999999999999999999999999999999 99999999999999888
Q ss_pred ----cchhhhcccc---------------------ccccccCCcccceeec---CCCCCchhhhhhh
Q psy16768 84 ----FDLIIMVSKS---------------------WMLDEVKSTTARSVTP---ACEPNSHHDVKKI 122 (154)
Q Consensus 84 ----~~R~Gm~~~~---------------------g~~D~l~svSa~Ii~G---~~GTG~~~~~~~~ 122 (154)
+-++|+.... ++.+.+.|++.+.++| ..|+|+.+.-.+.
T Consensus 680 ~~~~iG~~gv~g~r~~~~~~~~Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KT 746 (808)
T COG0086 680 IVQLIGQQGVMGEKISVLARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKT 746 (808)
T ss_pred HHHHhhhheeeccCCCcccccccccccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhh
Confidence 6666655322 8899999999999999 6789998887765
No 26
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=75.21 E-value=4 Score=33.12 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=34.6
Q ss_pred EEEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcC
Q psy16768 8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYG 64 (154)
Q Consensus 8 ~l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~G 64 (154)
.|.++|.|+-..|.. +..+.+..|.|+||..+|+.+.+-=+.+|
T Consensus 5 iLLVDGYNmIgaWp~-------------Lk~lkd~~~LE~AR~~LIe~l~~Y~s~~g 48 (173)
T COG3688 5 ILLVDGYNMIGAWPE-------------LKQLKDRNGLEAARDKLIEALAEYQSFTG 48 (173)
T ss_pred EEEeccchhccccHH-------------HHHHHhhccHHHHHHHHHHHHHHhhcccC
Confidence 578999998887765 37788889999999999999876433333
No 27
>PF08546 ApbA_C: Ketopantoate reductase PanE/ApbA C terminal; InterPro: IPR013752 This is the C-terminal domain of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, 1.1.1.169 from EC. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway []. ApbA and PanE are allelic []. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway []. ; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 1YJQ_A 1KS9_A 2OFP_A 1YON_A 2EW2_B 3EGO_B 3HN2_D 3GHY_B 3G17_E 3HWR_B ....
Probab=53.63 E-value=21 Score=25.75 Aligned_cols=56 Identities=18% Similarity=0.189 Sum_probs=36.5
Q ss_pred cHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhH-HHHHHHHHhhhccchhhhc
Q psy16768 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRH-LSLVADYMTHSEFDLIIMV 90 (154)
Q Consensus 35 dI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rH-i~LIaD~MT~~G~~R~Gm~ 90 (154)
+..++++.=+..+.-..+++|+..|.+..|+.++..+ .+.+.+.+...+-++..|.
T Consensus 26 ~~g~l~~~~~~~~~~~~l~~E~~~va~a~G~~l~~~~~~~~~~~~~~~~~~~~~SM~ 82 (125)
T PF08546_consen 26 TNGELLENPEARELIRALMREVIAVARALGIPLDPDDLEEAIERLIRSTPDNRSSML 82 (125)
T ss_dssp -HHHHHHSHHHHHHHHHHHHHHHHHHHHTTSS--HHHHHHHHHHHHHCTTTT--HHH
T ss_pred cHHHHHhChhHHHHHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHhcCCccccHH
Confidence 3466666677778888999999999999999999884 4455555544443344443
No 28
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=47.43 E-value=27 Score=25.12 Aligned_cols=36 Identities=8% Similarity=0.197 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhhhhcCcc--------cchhHHHHHHHHHhhh
Q psy16768 47 AANRVIIREVKNVFAVYGIE--------VDPRHLSLVADYMTHS 82 (154)
Q Consensus 47 AaR~~Ii~Ei~~v~~~~Gi~--------Vd~rHi~LIaD~MT~~ 82 (154)
+....-++++++++-.+++. .+.+++..|.|+|+.+
T Consensus 36 ~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~~y~~~t 79 (101)
T PF14769_consen 36 MSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAIIDYFHNT 79 (101)
T ss_pred CCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHHHHHHHH
Confidence 34455677888888888998 9999999999999876
No 29
>PF12335 SBF2: Myotubularin protein ; InterPro: IPR022096 This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with PF02141 from PFAM, PF03456 from PFAM, PF03455 from PFAM. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease.
Probab=39.96 E-value=68 Score=26.89 Aligned_cols=46 Identities=9% Similarity=0.146 Sum_probs=37.9
Q ss_pred HHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhh
Q psy16768 36 IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTH 81 (154)
Q Consensus 36 I~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~ 81 (154)
+..++..|..++||..+.+|+..-.....--++..-...|++.|-.
T Consensus 46 ~~av~~~lk~~~aR~~~~~~L~~~~~~~k~~L~~~qF~~lv~lin~ 91 (225)
T PF12335_consen 46 LPAVLRALKSRSARQAFCRELSKHVKSNKAVLDDQQFDYLVRLINC 91 (225)
T ss_pred HHHHHHHHccchHHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHH
Confidence 3566788999999999999999977665545899999999988754
No 30
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 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). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=37.33 E-value=13 Score=29.92 Aligned_cols=49 Identities=12% Similarity=0.038 Sum_probs=41.5
Q ss_pred cHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc
Q psy16768 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE 83 (154)
Q Consensus 35 dI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G 83 (154)
....+....+.+...++...+++.+|..+|+....||++.++-+|+..-
T Consensus 169 ~~~~~~~~~~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~ 217 (277)
T PF04998_consen 169 ISKDILEKKSKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKL 217 (277)
T ss_dssp EHHHHCEECCCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHH
T ss_pred eeeccccchhHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeE
Confidence 4566667777788888888999999999999999999999999999873
No 31
>PF13421 Band_7_1: SPFH domain-Band 7 family
Probab=35.55 E-value=57 Score=26.71 Aligned_cols=44 Identities=16% Similarity=0.275 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhhhhcCcccc--hhHHHHHHHHHhhhc---cchhhhc
Q psy16768 47 AANRVIIREVKNVFAVYGIEVD--PRHLSLVADYMTHSE---FDLIIMV 90 (154)
Q Consensus 47 AaR~~Ii~Ei~~v~~~~Gi~Vd--~rHi~LIaD~MT~~G---~~R~Gm~ 90 (154)
-.|..|+..+..++..+++++. ..|+.-|++.+...- +.++|+.
T Consensus 136 ~l~~~i~~~i~~~l~~~~~~~~~i~a~~~eis~~~~~~l~~~~~~~Gi~ 184 (211)
T PF13421_consen 136 QLRSEIVQAIADALAESKISILDIPAHLDEISEALKEKLNPEFERYGIE 184 (211)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCcE
Confidence 3456677778888888888888 799999999998875 8888875
No 32
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=29.88 E-value=56 Score=24.95 Aligned_cols=44 Identities=16% Similarity=0.275 Sum_probs=25.6
Q ss_pred HHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 36 IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 36 I~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
|.++++.|+ .-|..++.-++.+-+.+| .|...++..||+.+--.
T Consensus 1 i~~i~~~~~--~~~~~ll~~L~~~Q~~~g-~i~~~~~~~iA~~l~i~ 44 (145)
T PF01257_consen 1 IEEIIARYP--SKRSALLPILHEVQEEYG-YIPEEALEEIAEALGIP 44 (145)
T ss_dssp -HHHHHTS----GGGGHHHHHHHHHHHHS-S--HHHHHHHHHHHTS-
T ss_pred ChHHHHHCC--CCHHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHCCC
Confidence 345666666 444455555555555557 99999999999987544
No 33
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=29.30 E-value=1.2e+02 Score=23.36 Aligned_cols=44 Identities=23% Similarity=0.227 Sum_probs=32.5
Q ss_pred cHHHHHHhhC-HHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 35 DIHYMASTYG-IEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 35 dI~~i~~~lG-IEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
++.++++.|+ =.++--.+++++|+.| | .|...++..||+.|--.
T Consensus 9 ~~~~i~~~~~~~~~~ll~~L~~vQ~~~---g-~ip~~~~~~iA~~l~v~ 53 (154)
T PRK07539 9 AIEREIAKYPRPRSAVIPALKIVQEQR---G-WVPDEAIEAVADYLGMP 53 (154)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHh---C-CCCHHHHHHHHHHhCcC
Confidence 5788888887 4444445666666655 5 89999999999987544
No 34
>KOG1914|consensus
Probab=28.89 E-value=63 Score=31.14 Aligned_cols=57 Identities=16% Similarity=0.291 Sum_probs=41.7
Q ss_pred HHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 18 YISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 18 ~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
.++.. ..+|.+-++|+-+.-+.+.-|++|||..+.+--+..... +|+-+-|=+|-+.
T Consensus 356 ~ll~~-~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~-------hhVfVa~A~mEy~ 412 (656)
T KOG1914|consen 356 KLLKI-EDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTR-------HHVFVAAALMEYY 412 (656)
T ss_pred HHHhh-hccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCc-------chhhHHHHHHHHH
Confidence 45556 378999999999999999999999998776655544332 4565555555443
No 35
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=27.09 E-value=83 Score=24.09 Aligned_cols=43 Identities=19% Similarity=0.195 Sum_probs=29.0
Q ss_pred HHHHHHhhCH---HHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 36 IHYMASTYGI---EAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 36 I~~i~~~lGI---EAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
+.+++..|+- .++--.+++++|+. +| .|.+..+..||+.|--.
T Consensus 2 ~~~i~~~~~~~~~~~~li~~L~~vQ~~---~G-~i~~~~~~~iA~~l~~~ 47 (148)
T TIGR01958 2 IEEIIAKYPDDQKRSAIMPALMIAQEQ---KG-WVTPEAIAAVAEMLGIP 47 (148)
T ss_pred hHHHHHHCCCCCChhHHHHHHHHHHHH---hC-CCCHHHHHHHHHHhCcC
Confidence 3566677763 23334455556554 56 89999999999998654
No 36
>TIGR00745 apbA_panE 2-dehydropantoate 2-reductase. This model describes enzymes that perform as 2-dehydropantoate 2-reductase, one of four enzymes required for the de novo biosynthesis of pantothenate (vitamin B5) from Asp and 2-oxoisovalerate. Although few members of the seed alignment are characterized experimentally, nearly all from complete genomes are found in a genome-wide (but not local) context of all three other pantothenate-biosynthetic enzymes (TIGR00222, TIGR00018, TIGR00223). The gene encoding this enzyme is designated apbA in Salmonella typhimurium and panE in Escherichia coli; this protein functions as a monomer and functions in the alternative pyrimidine biosynthetic, or APB, pathway, used to synthesize the pyrimidine moiety of thiamine. Note, synthesis of the pyrimidine moiety of thiamine occurs either via the first five steps in de novo purine biosynthesis, which uses the pur gene products, or through the APB pathway. Note that this family includes both NADH and NADPH
Probab=26.81 E-value=77 Score=25.61 Aligned_cols=56 Identities=13% Similarity=0.141 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhhc-cchhhhcccc-----ccccccCC
Q psy16768 46 EAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSE-FDLIIMVSKS-----WMLDEVKS 101 (154)
Q Consensus 46 EAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G-~~R~Gm~~~~-----g~~D~l~s 101 (154)
.+.-..+++|+..|.+..|+.++...+.-..+.+.... -+|..|...- -|.|.+.|
T Consensus 203 ~~l~~~~~~E~~~v~~a~G~~~~~~~~~~~~~~~~~~~~~~~sSm~~D~~~gr~tEid~i~G 264 (293)
T TIGR00745 203 RELLRRLMDEVVRVARAEGVDLPDDEVEELVRAVIRMTAENTSSMLQDLLRGRRTEIDAING 264 (293)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCCCCChHHHHHHcCCcchHHHhcc
Confidence 34556689999999999999999987766666655433 4444443211 55565554
No 37
>CHL00077 rps18 ribosomal protein S18
Probab=24.88 E-value=37 Score=24.67 Aligned_cols=20 Identities=20% Similarity=0.539 Sum_probs=18.6
Q ss_pred CcccchhHHHHHHHHHhhhc
Q psy16768 64 GIEVDPRHLSLVADYMTHSE 83 (154)
Q Consensus 64 Gi~Vd~rHi~LIaD~MT~~G 83 (154)
+..||++.+.||..+++..|
T Consensus 25 ~~~iDYKnv~lL~~Fis~~G 44 (86)
T CHL00077 25 GDRIDYKNMSLLSRFISEQG 44 (86)
T ss_pred CCcCCccCHHHHHHhcCCCC
Confidence 45799999999999999999
No 38
>PF13096 CENP-P: CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P
Probab=22.81 E-value=45 Score=27.27 Aligned_cols=22 Identities=27% Similarity=0.265 Sum_probs=16.7
Q ss_pred eeccHHHHHHhhCHHHHHHHHH
Q psy16768 32 YVNDIHYMASTYGIEAANRVII 53 (154)
Q Consensus 32 ~sNdI~~i~~~lGIEAaR~~Ii 53 (154)
-+...+.++.++|||||-..+|
T Consensus 156 ap~~Fr~ll~~~Gieaa~E~lI 177 (177)
T PF13096_consen 156 APLSFRSLLGVLGIEAALESLI 177 (177)
T ss_pred ccHHHHHHHHHhhHHHHHHhcC
Confidence 3455678889999999977653
No 39
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=22.42 E-value=1.1e+02 Score=23.18 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=24.8
Q ss_pred HHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 54 REVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 54 ~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
+.|++|++.-|+.|+.--+.++++.|.-+
T Consensus 23 ddI~kIL~AaGveVd~~~~~l~~~~L~GK 51 (112)
T PTZ00373 23 KEVKNVLSAVNADVEDDVLDNFFKSLEGK 51 (112)
T ss_pred HHHHHHHHHcCCCccHHHHHHHHHHHcCC
Confidence 46788899999999999999999998433
No 40
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=21.82 E-value=1.1e+02 Score=22.77 Aligned_cols=27 Identities=30% Similarity=0.502 Sum_probs=23.7
Q ss_pred HHHHHhhhhcCcccchhHHHHHHHHHh
Q psy16768 54 REVKNVFAVYGIEVDPRHLSLVADYMT 80 (154)
Q Consensus 54 ~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT 80 (154)
+.|++|++.-|+.|+.--+.++++.|-
T Consensus 21 ~dI~~IL~AaGveVe~~~~~lf~~~L~ 47 (109)
T cd05833 21 ADVKKILGSVGVEVDDEKLNKVISELE 47 (109)
T ss_pred HHHHHHHHHcCCCccHHHHHHHHHHHc
Confidence 467888999999999999999999873
No 41
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=21.57 E-value=70 Score=25.02 Aligned_cols=40 Identities=23% Similarity=0.190 Sum_probs=25.2
Q ss_pred EEEecCChHHHhccCCccccCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhh
Q psy16768 9 LKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 61 (154)
Q Consensus 9 l~teG~nl~~~~~~~d~vD~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~ 61 (154)
|.++|.|+...|.. +......-..|+||..+++.+..--.
T Consensus 1 LlIDGYNli~~~~~-------------l~~~~~~~~l~~aR~~Li~~L~~y~~ 40 (166)
T PF05991_consen 1 LLIDGYNLIHAWPE-------------LRSLAERGDLEAARERLIEMLSEYAQ 40 (166)
T ss_pred CeEcchhhhCCCHH-------------HHhhcCcCCHHHHHHHHHHHHHHHhc
Confidence 34677776554332 12223344589999999999976443
No 42
>PF06505 XylR_N: Activator of aromatic catabolism; InterPro: IPR010523 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to IPR004096 from INTERPRO.
Probab=21.45 E-value=1e+02 Score=22.80 Aligned_cols=17 Identities=24% Similarity=0.325 Sum_probs=12.6
Q ss_pred HHHHHhhCHHHHHHHHH
Q psy16768 37 HYMASTYGIEAANRVII 53 (154)
Q Consensus 37 ~~i~~~lGIEAaR~~Ii 53 (154)
.|+.+++|.|+||..+.
T Consensus 35 kELi~~lG~~~AR~ilt 51 (103)
T PF06505_consen 35 KELIETLGEERARGILT 51 (103)
T ss_pred HHHHHHhCHHHHHHHHH
Confidence 57778888888885543
No 43
>PF10598 RRM_4: RNA recognition motif of the spliceosomal PrP8; InterPro: IPR019582 The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is the pre-mRNA-processing-splicing factor 8 (PrP8) which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa []. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RNA- recognition-motif (RRM) are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain [].
Probab=21.21 E-value=48 Score=24.50 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=13.0
Q ss_pred HHHHHhhhc-----------cchhhhcc
Q psy16768 75 VADYMTHSE-----------FDLIIMVS 91 (154)
Q Consensus 75 IaD~MT~~G-----------~~R~Gm~~ 91 (154)
||||||.+- .|++|+-+
T Consensus 20 iadYitaKnNv~i~yKDM~h~N~yGlir 47 (93)
T PF10598_consen 20 IADYITAKNNVVINYKDMNHTNSYGLIR 47 (93)
T ss_pred HHHHHHhhhcceEEEeccHHHhHhcccc
Confidence 789999886 67777654
No 44
>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
Probab=20.77 E-value=79 Score=30.17 Aligned_cols=48 Identities=17% Similarity=0.251 Sum_probs=36.4
Q ss_pred cCcceeccHHHHHHhhCHHHHHHHHHHHHHHhhhhcCcccchhHHHHH
Q psy16768 28 LNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLV 75 (154)
Q Consensus 28 ~~r~~sNdI~~i~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LI 75 (154)
.+-..|-.+..|+++-|++|||+.+++--+.-+-.+.|.|....|+--
T Consensus 396 ~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~ 443 (660)
T COG5107 396 LTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYY 443 (660)
T ss_pred hhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHH
Confidence 344567789999999999999999988777666666666666665543
No 45
>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....
Probab=20.53 E-value=28 Score=22.91 Aligned_cols=24 Identities=8% Similarity=0.263 Sum_probs=20.6
Q ss_pred CcccchhHHHHHHHHHhhhc--cchh
Q psy16768 64 GIEVDPRHLSLVADYMTHSE--FDLI 87 (154)
Q Consensus 64 Gi~Vd~rHi~LIaD~MT~~G--~~R~ 87 (154)
...||++...+|..+|+..| +.|.
T Consensus 4 ~~~idykn~~lL~~Fi~~~GkIl~rr 29 (54)
T PF01084_consen 4 NEYIDYKNVELLSQFISPTGKILPRR 29 (54)
T ss_dssp SSSSSSSSHHHHGCGBTTSSSBSTHH
T ss_pred CCcCCcCCHHHHHHHcCcccceehhh
Confidence 46799999999999999999 5554
No 46
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=20.39 E-value=14 Score=29.59 Aligned_cols=54 Identities=13% Similarity=0.209 Sum_probs=37.6
Q ss_pred HHHHHHhhCHHHHHHH-----HHHHHHHhhhhcCcccchhHHHHHHHHHhhhc--cchhhh
Q psy16768 36 IHYMASTYGIEAANRV-----IIREVKNVFAVYGIEVDPRHLSLVADYMTHSE--FDLIIM 89 (154)
Q Consensus 36 I~~i~~~lGIEAaR~~-----Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~G--~~R~Gm 89 (154)
+..+.+.+||.+.|.. =.+|+.+.|..++.-..++.+-+|.||+.=-- =||.|+
T Consensus 98 a~~~~~~lgIpvl~h~~kKP~~~~~i~~~~~~~~~~~~p~eiavIGDrl~TDVl~gN~~G~ 158 (168)
T PF09419_consen 98 AEALEKALGIPVLRHRAKKPGCFREILKYFKCQKVVTSPSEIAVIGDRLFTDVLMGNRMGS 158 (168)
T ss_pred HHHHHHhhCCcEEEeCCCCCccHHHHHHHHhhccCCCCchhEEEEcchHHHHHHHhhccCc
Confidence 5677888998864432 34677778877766678888888888875443 566664
No 47
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=20.33 E-value=2.4e+02 Score=22.48 Aligned_cols=44 Identities=14% Similarity=0.152 Sum_probs=31.8
Q ss_pred cHHHHHHhhC-HHHHHHHHHHHHHHhhhhcCcccchhHHHHHHHHHhhh
Q psy16768 35 DIHYMASTYG-IEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82 (154)
Q Consensus 35 dI~~i~~~lG-IEAaR~~Ii~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT~~ 82 (154)
.+.+++..|+ -.++--.+++++|+.| | .|.+.++..||+.|--.
T Consensus 23 ~i~~ii~~~~~~~~~li~~L~~iQ~~~---G-yIp~e~~~~iA~~l~v~ 67 (169)
T PRK07571 23 VLEATMKRNQYRQDALIEVLHKAQELF---G-YLERDLLLYVARQLKLP 67 (169)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHc---C-CCCHHHHHHHHHHhCcC
Confidence 4567777776 4444555666666655 5 89999999999998654
No 48
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=20.25 E-value=1.2e+02 Score=22.22 Aligned_cols=27 Identities=19% Similarity=0.406 Sum_probs=23.2
Q ss_pred HHHHHhhhhcCcccchhHHHHHHHHHh
Q psy16768 54 REVKNVFAVYGIEVDPRHLSLVADYMT 80 (154)
Q Consensus 54 ~Ei~~v~~~~Gi~Vd~rHi~LIaD~MT 80 (154)
+.|+++++.-|+.|+.--+.++++.|.
T Consensus 21 e~I~~ilkAaGveve~~~~~~f~~~L~ 47 (103)
T cd05831 21 DNINALLKAAGVNVEPYWPGLFAKALE 47 (103)
T ss_pred HHHHHHHHHcCCcccHHHHHHHHHHHc
Confidence 467888888899999999999999883
Done!