Query psy6966
Match_columns 155
No_of_seqs 121 out of 458
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 23:21:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6966hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02737 RNAP_IV_NRPD1_C Larges 99.7 7.4E-18 1.6E-22 148.8 6.7 83 73-155 184-292 (381)
2 cd02584 RNAP_II_Rpb1_C Largest 99.7 1.3E-17 2.8E-22 148.3 7.6 77 73-155 233-326 (410)
3 cd02736 RNAP_III_Rpc1_C Larges 99.7 1.7E-17 3.7E-22 142.4 7.4 65 88-155 149-221 (300)
4 TIGR02389 RNA_pol_rpoA2 DNA-di 99.7 4.1E-17 8.9E-22 143.5 6.8 71 74-155 205-283 (367)
5 PRK14897 unknown domain/DNA-di 99.7 4.5E-17 9.8E-22 148.7 7.1 74 73-155 338-419 (509)
6 cd02735 RNAP_I_Rpa1_C Largest 99.7 9.8E-17 2.1E-21 137.8 7.4 67 88-155 153-228 (309)
7 cd06528 RNAP_A'' A'' subunit o 99.7 1.5E-16 3.2E-21 139.6 6.7 72 73-155 199-278 (363)
8 PRK04309 DNA-directed RNA poly 99.6 2.8E-16 6E-21 138.7 7.2 64 87-155 224-295 (383)
9 PRK14977 bifunctional DNA-dire 99.6 3.2E-15 6.9E-20 147.9 7.3 75 74-155 1144-1226(1321)
10 PRK14898 DNA-directed RNA poly 99.6 4.1E-15 8.9E-20 141.5 7.5 75 74-155 683-765 (858)
11 KOG0262|consensus 99.6 2E-15 4.3E-20 148.9 4.4 81 71-154 1446-1551(1640)
12 KOG0260|consensus 99.5 2.1E-14 4.6E-19 141.4 3.6 76 74-155 1250-1335(1605)
13 KOG0261|consensus 99.3 1.3E-12 2.8E-17 127.4 2.4 66 86-154 1203-1276(1386)
14 PF04998 RNA_pol_Rpb1_5: RNA p 99.2 7.7E-12 1.7E-16 99.0 4.2 54 102-155 178-240 (277)
15 cd00630 RNAP_largest_subunit_C 98.8 4.9E-09 1.1E-13 83.5 4.2 32 124-155 49-80 (158)
16 cd02655 RNAP_beta'_C Largest s 98.0 9.1E-06 2E-10 67.4 4.3 38 115-155 49-88 (204)
17 COG0086 RpoC DNA-directed RNA 96.0 0.0012 2.6E-08 64.0 -1.1 52 103-154 601-660 (808)
18 PRK00566 DNA-directed RNA poly 95.8 0.0088 1.9E-07 60.4 4.1 33 123-155 989-1021(1156)
19 TIGR02386 rpoC_TIGR DNA-direct 95.7 0.011 2.5E-07 59.5 4.0 34 122-155 986-1019(1140)
20 PRK14844 bifunctional DNA-dire 93.7 0.064 1.4E-06 58.4 3.9 33 122-154 2635-2667(2836)
21 PRK02597 rpoC2 DNA-directed RN 87.4 0.65 1.4E-05 48.1 4.0 33 123-155 1059-1107(1331)
22 TIGR02388 rpoC2_cyan DNA-direc 78.2 2.5 5.4E-05 43.7 3.9 33 123-155 1058-1106(1227)
23 PRK14906 DNA-directed RNA poly 72.8 4 8.6E-05 43.0 3.8 33 122-154 1087-1119(1460)
24 CHL00117 rpoC2 RNA polymerase 57.2 9.7 0.00021 39.9 3.1 23 132-154 1181-1203(1364)
25 PRK09603 bifunctional DNA-dire 52.2 16 0.00035 41.1 3.8 32 123-154 2725-2756(2890)
26 PHA02335 hypothetical protein 49.9 9.6 0.00021 30.0 1.4 28 118-146 55-82 (118)
27 PF13096 CENP-P: CENP-A-nucleo 43.1 14 0.00031 30.9 1.5 18 125-142 160-177 (177)
28 PF07095 IgaA: Intracellular g 37.5 14 0.0003 36.5 0.7 12 58-69 292-303 (705)
29 cd01433 Ribosomal_L16_L10e Rib 36.5 29 0.00063 25.7 2.1 25 115-148 15-39 (112)
30 PF06505 XylR_N: Activator of 35.2 36 0.00078 25.6 2.4 18 126-143 35-52 (103)
31 smart00576 BTP Bromodomain tra 30.9 30 0.00066 24.0 1.4 28 125-152 12-39 (77)
32 PLN03236 4-alpha-glucanotransf 29.9 27 0.00059 34.5 1.3 20 1-20 102-125 (745)
33 PF00252 Ribosomal_L16: Riboso 29.9 48 0.001 25.5 2.4 25 115-148 36-60 (133)
34 CHL00044 rpl16 ribosomal prote 29.5 36 0.00078 26.7 1.7 24 115-147 37-60 (135)
35 PF08241 Methyltransf_11: Meth 29.4 20 0.00044 23.0 0.3 30 119-154 63-92 (95)
36 COG1640 MalQ 4-alpha-glucanotr 27.8 29 0.00064 33.0 1.1 20 1-20 55-76 (520)
37 PTZ00286 6-phospho-1-fructokin 26.8 26 0.00055 32.6 0.5 36 115-150 209-244 (459)
38 PRK14508 4-alpha-glucanotransf 26.6 35 0.00076 31.8 1.3 19 1-20 46-64 (497)
39 TIGR01164 rplP_bact ribosomal 26.4 44 0.00094 25.8 1.6 25 115-148 36-60 (126)
40 PRK09203 rplP 50S ribosomal pr 25.8 49 0.0011 25.9 1.9 26 114-148 36-61 (138)
41 PF10056 DUF2293: Uncharacteri 25.3 74 0.0016 23.4 2.6 30 124-153 56-86 (86)
42 TIGR00279 L10e ribosomal prote 23.4 70 0.0015 26.5 2.4 16 134-149 62-77 (172)
43 KOG1914|consensus 23.3 59 0.0013 32.0 2.2 36 108-143 356-391 (656)
44 PF03310 Cauli_DNA-bind: Cauli 23.3 1.1E+02 0.0025 24.1 3.4 30 121-150 18-55 (121)
45 PF00816 Histone_HNS: H-NS his 22.8 48 0.001 23.4 1.2 20 135-154 19-38 (93)
46 TIGR02482 PFKA_ATP 6-phosphofr 22.8 54 0.0012 28.6 1.7 40 111-150 115-154 (301)
47 PF00015 MCPsignal: Methyl-acc 22.4 88 0.0019 23.7 2.6 15 133-147 64-86 (213)
48 COG0332 FabH 3-oxoacyl-[acyl-c 22.3 1E+02 0.0022 27.5 3.3 38 101-143 29-66 (323)
49 COG0197 RplP Ribosomal protein 21.5 73 0.0016 25.8 2.1 14 134-147 50-63 (146)
50 PRK14510 putative bifunctional 20.8 48 0.001 34.3 1.1 19 1-20 765-787 (1221)
51 PRK04199 rpl10e 50S ribosomal 20.6 81 0.0018 26.1 2.3 16 134-149 62-77 (172)
No 1
>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=99.72 E-value=7.4e-18 Score=148.79 Aligned_cols=83 Identities=11% Similarity=0.012 Sum_probs=67.6
Q ss_pred EEeecccccc--cccC--CcceEEEcCCCCcCCccceEEecc---------cc-------------ceeeeceeeccCHH
Q psy6966 73 ILPLTGVSHP--LDLH--PSVLLLEGTTGSYGPEGTWIHDPL---------YG-------------LRGGVILDYHLLVL 126 (155)
Q Consensus 73 ~LpL~g~~~i--~dl~--~~~RavI~edg~~~~~~e~~LeTe---------Gt-------------~gVD~~RTySNDI~ 126 (155)
.+.|+|..+| +++. +..+..+.+++.++..+||+|+|+ |. ++||.+|++||||.
T Consensus 184 ~~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ 263 (381)
T cd02737 184 ETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQ 263 (381)
T ss_pred heeecccCCeeEEEEEecCCCcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHH
Confidence 3778888776 5554 444444444444566689999988 75 78999999999999
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 127 ETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 127 EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
||+++|||||||++|++||++||++||+|
T Consensus 264 ev~~~lGIEAAR~~ii~El~~v~~~~G~~ 292 (381)
T cd02737 264 QIKSVLGIDAAFEQFVQRLESAVSMTGKS 292 (381)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHhcCCc
Confidence 99999999999999999999999999986
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=99.71 E-value=1.3e-17 Score=148.32 Aligned_cols=77 Identities=26% Similarity=0.318 Sum_probs=63.6
Q ss_pred EEeecccccccccCCcceEEEcC---------CCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHH
Q psy6966 73 ILPLTGVSHPLDLHPSVLLLEGT---------TGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIE 135 (155)
Q Consensus 73 ~LpL~g~~~i~dl~~~~RavI~e---------dg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIE 135 (155)
.+.|.|.++ .+|+++.+ .|.++...+|+|+|+|+ ++||.+||+||||+||+++||||
T Consensus 233 ~i~l~Gi~~------I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIE 306 (410)
T cd02584 233 DMTLKGIEG------IRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIE 306 (410)
T ss_pred CcEEeCCCC------ceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHH
Confidence 466777665 34444432 34444456899999998 78999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcCCC
Q psy6966 136 AVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 136 AAR~aIIkEI~~Vf~~yGsY 155 (155)
|||++|++||++||+.||+|
T Consensus 307 AaR~~ii~Ei~~v~~~~Gi~ 326 (410)
T cd02584 307 AARKALLKELRNVISFDGSY 326 (410)
T ss_pred HHHHHHHHHHHHHHHhcCCc
Confidence 99999999999999999986
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=99.71 E-value=1.7e-17 Score=142.40 Aligned_cols=65 Identities=17% Similarity=0.052 Sum_probs=58.0
Q ss_pred cceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 88 SVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 88 ~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
.+|+++.+++ ..++|.|+|+|+ ++||.+|++||||.||+++|||||||++|++||++||+.||++
T Consensus 149 I~r~~i~~~~---~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~ 221 (300)
T cd02736 149 VKRAVINKDK---KKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMS 221 (300)
T ss_pred ceEEEEecCC---CCCcEEEEEecccHHHHhcCCcEeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCc
Confidence 5588886543 135799999998 8899999999999999999999999999999999999999975
No 4
>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=99.68 E-value=4.1e-17 Score=143.51 Aligned_cols=71 Identities=20% Similarity=0.151 Sum_probs=61.3
Q ss_pred EeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHH
Q psy6966 74 LPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEM 145 (155)
Q Consensus 74 LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI 145 (155)
+.+.|.++ .+||++.++ .++|+|+|+|+ ++||.+||+||||+||+++|||||||++|++||
T Consensus 205 ~~v~Gi~g------I~r~~i~~~-----~~~~~l~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei 273 (367)
T TIGR02389 205 LHIKGIKG------IKRVVIRKE-----GDEYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEI 273 (367)
T ss_pred ceEeCCCC------ceEEEEECC-----CCeEEEEEeccCHHHHHcCCCCccccCccCCHHHHHHhcCHHHHHHHHHHHH
Confidence 44555554 668888643 24799999998 889999999999999999999999999999999
Q ss_pred HHHhhhcCCC
Q psy6966 146 NTVLQFYGLY 155 (155)
Q Consensus 146 ~~Vf~~yGsY 155 (155)
++||+.||++
T Consensus 274 ~~v~~~~Gi~ 283 (367)
T TIGR02389 274 KRTLEEQGLD 283 (367)
T ss_pred HHHHHHcCCe
Confidence 9999999985
No 5
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=99.68 E-value=4.5e-17 Score=148.74 Aligned_cols=74 Identities=24% Similarity=0.278 Sum_probs=64.3
Q ss_pred EEeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHH
Q psy6966 73 ILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKE 144 (155)
Q Consensus 73 ~LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkE 144 (155)
.+.|.|+++ ..||++++++ ...+|+|+|+|+ ++||.+||+||||+||+++|||||||++|++|
T Consensus 338 ~i~I~Gipg------I~r~~i~~~~---~~~~~~L~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~E 408 (509)
T PRK14897 338 SLTIKGIKG------IKRAIARKEN---DERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHE 408 (509)
T ss_pred ccEEeCCCC------ccEEEEecCC---CCceeEEEeeccCHHHHhcCCCcccccCccCCHHHHHHhcCHHHHHHHHHHH
Confidence 466667665 7788887543 234699999998 88999999999999999999999999999999
Q ss_pred HHHHhhhcCCC
Q psy6966 145 MNTVLQFYGLY 155 (155)
Q Consensus 145 I~~Vf~~yGsY 155 (155)
|++||+.||+|
T Consensus 409 i~~V~~~~Gi~ 419 (509)
T PRK14897 409 AKRTLQEQGLN 419 (509)
T ss_pred HHHHHHhcCCc
Confidence 99999999986
No 6
>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=99.67 E-value=9.8e-17 Score=137.80 Aligned_cols=67 Identities=18% Similarity=0.087 Sum_probs=58.4
Q ss_pred cceEEEcCCCCcCCccceEEecccc---------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 88 SVLLLEGTTGSYGPEGTWIHDPLYG---------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 88 ~~RavI~edg~~~~~~e~~LeTeGt---------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
.+||++++++.. ...+|+|+|+|+ ++||.+|++||||+||+++|||||||++|++|+++||+.||.+
T Consensus 153 I~r~~i~~~~~~-~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~ 228 (309)
T cd02735 153 ITRCFVVEEDKG-GKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIA 228 (309)
T ss_pred ccEEEEecCcCC-CceEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCe
Confidence 678888754321 234799999998 5799999999999999999999999999999999999999975
No 7
>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=99.65 E-value=1.5e-16 Score=139.62 Aligned_cols=72 Identities=18% Similarity=0.122 Sum_probs=62.8
Q ss_pred EEeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHH
Q psy6966 73 ILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKE 144 (155)
Q Consensus 73 ~LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkE 144 (155)
.+.|.|.++ .+|+++.++. ++|+|+|+|+ ++||.+||+||||.||+++|||||||++|++|
T Consensus 199 ~~~v~Gi~g------I~r~~i~~~~-----~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~E 267 (363)
T cd06528 199 NTKIKGIKG------IKRVIVRKEE-----DEYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINE 267 (363)
T ss_pred ccEEeCCCC------ceEEEEecCC-----ceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHH
Confidence 455666665 6788886542 3799999998 78999999999999999999999999999999
Q ss_pred HHHHhhhcCCC
Q psy6966 145 MNTVLQFYGLY 155 (155)
Q Consensus 145 I~~Vf~~yGsY 155 (155)
|++||+.||.+
T Consensus 268 i~~v~~~~Gi~ 278 (363)
T cd06528 268 IKRTLEEQGLD 278 (363)
T ss_pred HHHHHHhcCCe
Confidence 99999999975
No 8
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=99.64 E-value=2.8e-16 Score=138.71 Aligned_cols=64 Identities=19% Similarity=0.105 Sum_probs=57.9
Q ss_pred CcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 87 PSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 87 ~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
..+|+++.++ .++|.|+|+|+ ++||.+||+||||+||+++|||||||++|++||++||+.||++
T Consensus 224 gI~r~~i~~~-----~~~~~l~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~ 295 (383)
T PRK04309 224 GIKRVIIRKE-----GDEYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLD 295 (383)
T ss_pred CceEEEEecC-----CCeEEEEEcccCHHHHhcCCCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCe
Confidence 3678888754 24799999998 8899999999999999999999999999999999999999975
No 9
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=99.57 E-value=3.2e-15 Score=147.89 Aligned_cols=75 Identities=21% Similarity=0.202 Sum_probs=62.1
Q ss_pred EeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHH
Q psy6966 74 LPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEM 145 (155)
Q Consensus 74 LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI 145 (155)
+.+.|.++ .+|++++.... ....+|+|+|+|+ ++||..||+||||+||+++|||||||++|++||
T Consensus 1144 ~~i~Gi~~------I~r~~i~~~~~-~~~~e~~l~teG~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei 1216 (1321)
T PRK14977 1144 KPVKGVPD------IERAWVELVEK-DGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNEL 1216 (1321)
T ss_pred cEEecCCC------ceEEEEEeecc-CCCeeEEEEecCcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHH
Confidence 45556554 67877753211 1225899999998 889999999999999999999999999999999
Q ss_pred HHHhhhcCCC
Q psy6966 146 NTVLQFYGLY 155 (155)
Q Consensus 146 ~~Vf~~yGsY 155 (155)
++||++||+|
T Consensus 1217 ~~v~~~~G~~ 1226 (1321)
T PRK14977 1217 ASILEDQGLE 1226 (1321)
T ss_pred HHHHHHcCCc
Confidence 9999999986
No 10
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.57 E-value=4.1e-15 Score=141.50 Aligned_cols=75 Identities=21% Similarity=0.187 Sum_probs=62.8
Q ss_pred EeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHH
Q psy6966 74 LPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEM 145 (155)
Q Consensus 74 LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI 145 (155)
+.|.|+++ ..||++.++.. +...+|+|+|+|+ ++||.+||+||||+||+++|||||||++|++||
T Consensus 683 ~~i~gi~g------I~~~~i~~~~~-~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei 755 (858)
T PRK14898 683 IVLKGIPG------IERVLVKKEEH-ENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEM 755 (858)
T ss_pred cEEECCCC------ccEEEEecCCC-CCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHHHHHHHHH
Confidence 44555554 67888875431 1235899999998 789999999999999999999999999999999
Q ss_pred HHHhhhcCCC
Q psy6966 146 NTVLQFYGLY 155 (155)
Q Consensus 146 ~~Vf~~yGsY 155 (155)
++||+.||++
T Consensus 756 ~~v~~~~gi~ 765 (858)
T PRK14898 756 MNTLEQQGLE 765 (858)
T ss_pred HHHHHhcCCc
Confidence 9999999975
No 11
>KOG0262|consensus
Probab=99.56 E-value=2e-15 Score=148.89 Aligned_cols=81 Identities=22% Similarity=0.187 Sum_probs=66.8
Q ss_pred ceEEeecccccccccCCcc----------------eEEEcCCCCcCCccceEEecccc---------ceeeeceeeccCH
Q psy6966 71 PFILPLTGVSHPLDLHPSV----------------LLLEGTTGSYGPEGTWIHDPLYG---------LRGGVILDYHLLV 125 (155)
Q Consensus 71 ~f~LpL~g~~~i~dl~~~~----------------RavI~edg~~~~~~e~~LeTeGt---------~gVD~~RTySNDI 125 (155)
.|.+|+...+ +||.+.+ ||++.+.+...+... +|.|+|+ +.+|++++|||||
T Consensus 1446 ~~~lp~~~~k--~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~-~l~TeGVnl~a~~~~~d~LDv~~lySNDI 1522 (1640)
T KOG0262|consen 1446 ELKLPLDKEK--LDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKS-VLLTEGVNLPALFDHADILDVNRLYSNDI 1522 (1640)
T ss_pred EEEecCCCcc--hHHHHHHHHHhcceeeeccCCceeeeccCCcccccccc-eehhcCccHHHHHHHHhhhhhhhhccchH
Confidence 5778887666 8885544 787765443333334 8999998 5699999999999
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 126 LETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 126 ~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
++|+++|||||||++|++||++||++||+
T Consensus 1523 ~ail~tyGVEAar~~Iv~Ev~~VF~vYGI 1551 (1640)
T KOG0262|consen 1523 HAILNTYGVEAARNAIVNEVNNVFKVYGI 1551 (1640)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHhhhheee
Confidence 99999999999999999999999999996
No 12
>KOG0260|consensus
Probab=99.47 E-value=2.1e-14 Score=141.41 Aligned_cols=76 Identities=26% Similarity=0.341 Sum_probs=66.9
Q ss_pred EeecccccccccCCcceEEE--cCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966 74 LPLTGVSHPLDLHPSVLLLE--GTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEK 143 (155)
Q Consensus 74 LpL~g~~~i~dl~~~~RavI--~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk 143 (155)
|+|+|..+| .|+++ .++|.+....+|+|+|+|+ ++||..||+|||+.||+++|||||+|+++++
T Consensus 1250 ~~l~G~~~i------~kV~m~~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~ 1323 (1605)
T KOG0260|consen 1250 MTLRGIPDI------FKVYMSPTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLR 1323 (1605)
T ss_pred cccCCcccc------ceEEEeecCCCceeecceeEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhh
Confidence 777777764 34443 4578787778999999998 7899999999999999999999999999999
Q ss_pred HHHHHhhhcCCC
Q psy6966 144 EMNTVLQFYGLY 155 (155)
Q Consensus 144 EI~~Vf~~yGsY 155 (155)
|+.+|+.++|+|
T Consensus 1324 e~~~vi~f~gsy 1335 (1605)
T KOG0260|consen 1324 ELLNVISFDGSY 1335 (1605)
T ss_pred hhhheEeecccc
Confidence 999999999998
No 13
>KOG0261|consensus
Probab=99.27 E-value=1.3e-12 Score=127.41 Aligned_cols=66 Identities=20% Similarity=0.032 Sum_probs=54.4
Q ss_pred CCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 86 HPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 86 ~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
-+.+|++|+.|+.- +-|-|-+||+ +||+++||.||++.||.+||||||||.+||+||.++|+.||+
T Consensus 1203 p~vnr~vi~~de~~---~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGm 1276 (1386)
T KOG0261|consen 1203 PEVNRAVINIDEKR---GLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGM 1276 (1386)
T ss_pred cchhhhheeecccC---CceEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCc
Confidence 45678988765321 1144445553 899999999999999999999999999999999999999997
No 14
>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=99.23 E-value=7.7e-12 Score=99.04 Aligned_cols=54 Identities=22% Similarity=0.199 Sum_probs=50.6
Q ss_pred ccceEEecccc--------ce-eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 102 EGTWIHDPLYG--------LR-GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 102 ~~e~~LeTeGt--------~g-VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
..+|+++++|. ++ +|.+|+++|||.+|+++|||||||++|++|++.||..||.+
T Consensus 178 ~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~ 240 (277)
T PF04998_consen 178 SKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIE 240 (277)
T ss_dssp CCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSC
T ss_pred hHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHH
Confidence 35899999997 77 99999999999999999999999999999999999999964
No 15
>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=98.79 E-value=4.9e-09 Score=83.45 Aligned_cols=32 Identities=34% Similarity=0.475 Sum_probs=31.0
Q ss_pred CHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 124 LVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 124 DI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
||.+|+++|||||||+.|++||++||+.||.+
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~ 80 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVS 80 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCce
Confidence 99999999999999999999999999999974
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=97.96 E-value=9.1e-06 Score=67.37 Aligned_cols=38 Identities=21% Similarity=0.142 Sum_probs=34.6
Q ss_pred eeeceeeccCHHHHHHHH--hHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 115 GGVILDYHLLVLETTIVL--GIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 115 VD~~RTySNDI~EI~~VL--GIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
++..+ ||++++++++ ||||||+.|++||++|+..||.+
T Consensus 49 ~e~r~---~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~ 88 (204)
T cd02655 49 FEARK---INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVN 88 (204)
T ss_pred HHhhc---CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCee
Confidence 55555 9999999999 99999999999999999999975
No 17
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=96.00 E-value=0.0012 Score=63.99 Aligned_cols=52 Identities=25% Similarity=0.300 Sum_probs=46.6
Q ss_pred cceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 103 GTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 103 ~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
.+|+.+++|. +++|.+++.+||+.|++.++|+||+|+++++|+..+++..|.
T Consensus 601 ~e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~ 660 (808)
T COG0086 601 DEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGL 660 (808)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCC
Confidence 3688888886 679999999999999999999999999999999998876664
No 18
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=95.84 E-value=0.0088 Score=60.37 Aligned_cols=33 Identities=27% Similarity=0.391 Sum_probs=30.5
Q ss_pred cCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 123 LLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 123 NDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
=|++||++++||||+|+.|++||++|+..+|.+
T Consensus 989 ~~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~ 1021 (1156)
T PRK00566 989 IDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVK 1021 (1156)
T ss_pred CCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcc
Confidence 359999999999999999999999999999963
No 19
>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=95.66 E-value=0.011 Score=59.53 Aligned_cols=34 Identities=24% Similarity=0.320 Sum_probs=31.3
Q ss_pred ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
+-|++||++++||||+|+.|++||++|+..+|.+
T Consensus 986 ~~~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~ 1019 (1140)
T TIGR02386 986 SIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVE 1019 (1140)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcc
Confidence 4579999999999999999999999999999853
No 20
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=93.69 E-value=0.064 Score=58.37 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=31.2
Q ss_pred ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
+.|.++|++++||||+|+.|++||+.|+..+|.
T Consensus 2635 ~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV 2667 (2836)
T PRK14844 2635 DPDLHDILRVLGLEALAHYMISEIQQVYRLQGV 2667 (2836)
T ss_pred CCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCe
Confidence 568999999999999999999999999999985
No 21
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=87.37 E-value=0.65 Score=48.08 Aligned_cols=33 Identities=15% Similarity=0.172 Sum_probs=30.2
Q ss_pred cCHHHHHHH----------------HhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 123 LLVLETTIV----------------LGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 123 NDI~EI~~V----------------LGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
.|.++++++ +|+||+|..+++|+++|++++|.|
T Consensus 1059 ~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~ 1107 (1331)
T PRK02597 1059 INPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVD 1107 (1331)
T ss_pred CCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeE
Confidence 677888888 899999999999999999999975
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=78.20 E-value=2.5 Score=43.70 Aligned_cols=33 Identities=18% Similarity=0.177 Sum_probs=28.7
Q ss_pred cCHHHHHHH----------------HhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966 123 LLVLETTIV----------------LGIEAVRKSVEKEMNTVLQFYGLY 155 (155)
Q Consensus 123 NDI~EI~~V----------------LGIEAAR~aIIkEI~~Vf~~yGsY 155 (155)
+|.++++++ +|+||+|..|++||++|++.+|.+
T Consensus 1058 ~~ph~iL~~~~~~~~~~~g~~~aa~~s~~~~q~~lv~eiq~vy~~QGv~ 1106 (1227)
T TIGR02388 1058 INPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVD 1106 (1227)
T ss_pred CCHHHHHhhhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhcceE
Confidence 566777777 499999999999999999999963
No 23
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=72.80 E-value=4 Score=42.97 Aligned_cols=33 Identities=6% Similarity=0.021 Sum_probs=30.2
Q ss_pred ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
+=|.++++++.|+||+.+-|++|+++|...+|-
T Consensus 1087 ~~~p~~il~~~g~~~~~~ylv~eVQ~VYr~QGV 1119 (1460)
T PRK14906 1087 SVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGV 1119 (1460)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCc
Confidence 346899999999999999999999999999884
No 24
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=57.19 E-value=9.7 Score=39.93 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=21.1
Q ss_pred HhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 132 LGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 132 LGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
+.|||+|..|++||++|++.+|.
T Consensus 1181 lS~~~~~~~lv~eiq~vy~~qGv 1203 (1364)
T CHL00117 1181 LSIAQSQISLVNKIQKVYRSQGV 1203 (1364)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCc
Confidence 35999999999999999999995
No 25
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=52.23 E-value=16 Score=41.14 Aligned_cols=32 Identities=16% Similarity=0.191 Sum_probs=29.4
Q ss_pred cCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 123 LLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 123 NDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
=|.++|++++|+||..+-|++||++|...+|-
T Consensus 2725 ~~p~dil~~~g~~~~~~ylv~EVQ~VYr~QGV 2756 (2890)
T PRK09603 2725 VSSHDILRISGEKELYKYIVSEVQQVYRRQGV 2756 (2890)
T ss_pred CCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCE
Confidence 36899999999999999999999999998884
No 26
>PHA02335 hypothetical protein
Probab=49.86 E-value=9.6 Score=30.03 Aligned_cols=28 Identities=14% Similarity=-0.008 Sum_probs=23.4
Q ss_pred ceeeccCHHHHHHHHhHHHHHHHHHHHHH
Q psy6966 118 ILDYHLLVLETTIVLGIEAVRKSVEKEMN 146 (155)
Q Consensus 118 ~RTySNDI~EI~~VLGIEAAR~aIIkEI~ 146 (155)
+|..-|++.-+++||| |||-..++.-..
T Consensus 55 ~hlIlNhlI~l~NvF~-eAa~plLfyKte 82 (118)
T PHA02335 55 THLILNHIIILYNVFG-EAATPLLFYKLE 82 (118)
T ss_pred HHHHHHHHHHHHHhhh-hhhhhhhHHhhh
Confidence 5778899999999999 999887765443
No 27
>PF13096 CENP-P: CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P
Probab=43.13 E-value=14 Score=30.88 Aligned_cols=18 Identities=39% Similarity=0.287 Sum_probs=14.2
Q ss_pred HHHHHHHHhHHHHHHHHH
Q psy6966 125 VLETTIVLGIEAVRKSVE 142 (155)
Q Consensus 125 I~EI~~VLGIEAAR~aII 142 (155)
.-..+.+||||||-+.+|
T Consensus 160 Fr~ll~~~Gieaa~E~lI 177 (177)
T PF13096_consen 160 FRSLLGVLGIEAALESLI 177 (177)
T ss_pred HHHHHHHhhHHHHHHhcC
Confidence 445788999999987754
No 28
>PF07095 IgaA: Intracellular growth attenuator protein IgaA; InterPro: IPR010771 This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the Escherichia coli YrfF and Proteus mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in Salmonella enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria [].; GO: 0009276 Gram-negative-bacterium-type cell wall, 0016021 integral to membrane
Probab=37.52 E-value=14 Score=36.47 Aligned_cols=12 Identities=67% Similarity=1.483 Sum_probs=10.2
Q ss_pred CCCcCccccCCC
Q psy6966 58 PPHWTPYIRPDP 69 (155)
Q Consensus 58 ~~~~~~~~~~~~ 69 (155)
|+||.|||.-|-
T Consensus 292 P~HWqPyi~~dl 303 (705)
T PF07095_consen 292 PPHWQPYIAYDL 303 (705)
T ss_pred CccccccccccC
Confidence 899999997663
No 29
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=36.52 E-value=29 Score=25.72 Aligned_cols=25 Identities=12% Similarity=-0.077 Sum_probs=19.0
Q ss_pred eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHH
Q psy6966 115 GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTV 148 (155)
Q Consensus 115 VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~V 148 (155)
.+..++.+|. |||||.+|.+.++..
T Consensus 15 ~e~~~i~~~~---------lEa~R~~i~r~l~k~ 39 (112)
T cd01433 15 LEPGRITAEQ---------LEAARIAINRYLKKK 39 (112)
T ss_pred CcCCeECHHH---------HHHHHHHHHHHhhhc
Confidence 3444666665 599999999999876
No 30
>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=35.19 E-value=36 Score=25.61 Aligned_cols=18 Identities=28% Similarity=0.263 Sum_probs=15.2
Q ss_pred HHHHHHHhHHHHHHHHHH
Q psy6966 126 LETTIVLGIEAVRKSVEK 143 (155)
Q Consensus 126 ~EI~~VLGIEAAR~aIIk 143 (155)
.|..++||.|+||..+.+
T Consensus 35 kELi~~lG~~~AR~iltR 52 (103)
T PF06505_consen 35 KELIETLGEERARGILTR 52 (103)
T ss_pred HHHHHHhCHHHHHHHHHH
Confidence 588899999999987754
No 31
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=30.90 E-value=30 Score=23.96 Aligned_cols=28 Identities=21% Similarity=0.359 Sum_probs=23.9
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHhhhc
Q psy6966 125 VLETTIVLGIEAVRKSVEKEMNTVLQFY 152 (155)
Q Consensus 125 I~EI~~VLGIEAAR~aIIkEI~~Vf~~y 152 (155)
|..|++.-|.|.++.+-++.+.++++.|
T Consensus 12 Vaqil~~~Gf~~~~~sale~ltdi~~~y 39 (77)
T smart00576 12 VAQILESAGFDSFQESALETLTDILQSY 39 (77)
T ss_pred HHHHHHHcCccccCHHHHHHHHHHHHHH
Confidence 5678888899999999999999888766
No 32
>PLN03236 4-alpha-glucanotransferase; Provisional
Probab=29.90 E-value=27 Score=34.55 Aligned_cols=20 Identities=35% Similarity=0.554 Sum_probs=15.0
Q ss_pred CCCCcccccC----CCCCCccccc
Q psy6966 1 MLPLHPLILP----PSSPYSCTST 20 (155)
Q Consensus 1 ~~~~~~~~~~----~~~~~~~~~~ 20 (155)
+||||+.-.. -||||||.|.
T Consensus 102 iLPL~~t~~~~~~~dSSPYsp~S~ 125 (745)
T PLN03236 102 LLPVNDTCVHGTFWDSYPYSSLSV 125 (745)
T ss_pred ECCCCcCCCCCCCCCCCCcCcccc
Confidence 5899997532 3589999886
No 33
>PF00252 Ribosomal_L16: Ribosomal protein L16p/L10e; InterPro: IPR016180 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 entry represents a structural domain with an alpha/beta-hammerhead fold, where the beta-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2ZJR_J 1Y69_K 3DLL_J 2ZJQ_J 2ZJP_J 3PIO_J 3CF5_J 3PIP_J 2ZKR_h 3J11_O ....
Probab=29.88 E-value=48 Score=25.49 Aligned_cols=25 Identities=12% Similarity=-0.081 Sum_probs=19.0
Q ss_pred eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHH
Q psy6966 115 GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTV 148 (155)
Q Consensus 115 VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~V 148 (155)
.+.-++.+|. |||||.+|.+.|+..
T Consensus 36 ~~~g~l~~~q---------lEa~R~~i~r~lkk~ 60 (133)
T PF00252_consen 36 LEPGRLTSNQ---------LEAARIAINRYLKKN 60 (133)
T ss_dssp SS-EEEEHHH---------HHHHHHHHHHHHHHT
T ss_pred eeeeeechhh---------hHHHHHHHHHHhhhh
Confidence 4555677776 599999999999873
No 34
>CHL00044 rpl16 ribosomal protein L16
Probab=29.52 E-value=36 Score=26.66 Aligned_cols=24 Identities=17% Similarity=-0.006 Sum_probs=19.1
Q ss_pred eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHH
Q psy6966 115 GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNT 147 (155)
Q Consensus 115 VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~ 147 (155)
.+..++.+|. |||||.+|.+.|+.
T Consensus 37 ~e~~~i~~~q---------iEaaR~~i~r~lkk 60 (135)
T CHL00044 37 LEPAWITSRQ---------IEAGRRAITRYARR 60 (135)
T ss_pred ccCcEECHHH---------HHHHHHHHHHhhhc
Confidence 4556777776 59999999999976
No 35
>PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B ....
Probab=29.39 E-value=20 Score=22.97 Aligned_cols=30 Identities=20% Similarity=0.151 Sum_probs=24.7
Q ss_pred eeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966 119 LDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 119 RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs 154 (155)
.+++++..+-. .-+..+++|+..+++..|.
T Consensus 63 ~v~~~~~~~~~------~~~~~~l~e~~rvLk~gG~ 92 (95)
T PF08241_consen 63 VVFSNSVLHHL------EDPEAALREIYRVLKPGGR 92 (95)
T ss_dssp EEEEESHGGGS------SHHHHHHHHHHHHEEEEEE
T ss_pred ccccccceeec------cCHHHHHHHHHHHcCcCeE
Confidence 45888887766 7789999999999998774
No 36
>COG1640 MalQ 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]
Probab=27.84 E-value=29 Score=32.99 Aligned_cols=20 Identities=45% Similarity=0.570 Sum_probs=15.1
Q ss_pred CCCCcccccCC--CCCCccccc
Q psy6966 1 MLPLHPLILPP--SSPYSCTST 20 (155)
Q Consensus 1 ~~~~~~~~~~~--~~~~~~~~~ 20 (155)
++|+|++-.-. +||||+.|.
T Consensus 55 i~Plh~~~~~~~~~SPYs~~S~ 76 (520)
T COG1640 55 ILPLHATGPAYEEDSPYSPSSR 76 (520)
T ss_pred eccCCcccccccCCCCCCchhh
Confidence 47888877444 789998875
No 37
>PTZ00286 6-phospho-1-fructokinase; Provisional
Probab=26.80 E-value=26 Score=32.59 Aligned_cols=36 Identities=6% Similarity=0.041 Sum_probs=31.7
Q ss_pred eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhh
Q psy6966 115 GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQ 150 (155)
Q Consensus 115 VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~ 150 (155)
|-.=+|.-|||..+-.++|-++|.+.+.+-|+++..
T Consensus 209 IGIPKTIDNDI~~td~S~GFdTAv~~~~~aI~~~~~ 244 (459)
T PTZ00286 209 VGIPKTIDNDIPIIDESFGFQTAVEEAQNAIRAAYV 244 (459)
T ss_pred EEeccccCCCCCCcccCcCchHHHHHHHHHHHHHHH
Confidence 566699999999999999999999999998887643
No 38
>PRK14508 4-alpha-glucanotransferase; Provisional
Probab=26.60 E-value=35 Score=31.76 Aligned_cols=19 Identities=42% Similarity=0.576 Sum_probs=15.4
Q ss_pred CCCCcccccCCCCCCccccc
Q psy6966 1 MLPLHPLILPPSSPYSCTST 20 (155)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~ 20 (155)
+|||||.- .-.|||++.|.
T Consensus 46 ilPl~~~~-~~~SPY~~~S~ 64 (497)
T PRK14508 46 ILPLGPTG-YGDSPYQSFSA 64 (497)
T ss_pred EcCCCCCC-CCCCCcCcccc
Confidence 58999987 55679999875
No 39
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=26.42 E-value=44 Score=25.82 Aligned_cols=25 Identities=16% Similarity=-0.102 Sum_probs=18.9
Q ss_pred eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHH
Q psy6966 115 GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTV 148 (155)
Q Consensus 115 VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~V 148 (155)
.+..++.+|. |||||.+|.+-|+.-
T Consensus 36 ~e~~~i~~~q---------lEaaR~~i~r~l~~~ 60 (126)
T TIGR01164 36 LEPGWITARQ---------IEAARVAMTRYVKRG 60 (126)
T ss_pred CcCCeEcHHH---------HHHHHHHHHHHHhhC
Confidence 5556666665 599999999988753
No 40
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=25.83 E-value=49 Score=25.92 Aligned_cols=26 Identities=15% Similarity=-0.060 Sum_probs=19.4
Q ss_pred eeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHH
Q psy6966 114 RGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTV 148 (155)
Q Consensus 114 gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~V 148 (155)
-.+..++.+|. |||||.+|.+.++..
T Consensus 36 a~e~g~i~~~q---------lEaaR~~i~r~Lkk~ 61 (138)
T PRK09203 36 ALEPGWITARQ---------IEAARIAMTRHIKRG 61 (138)
T ss_pred ECcCCeEcHHH---------HHHHHHHHHHHhhcC
Confidence 34555666766 599999999998753
No 41
>PF10056 DUF2293: Uncharacterized conserved protein (DUF2293); InterPro: IPR018744 Proteins in this entry are found the bacteria and fungi, they have no known function.
Probab=25.27 E-value=74 Score=23.41 Aligned_cols=30 Identities=17% Similarity=0.090 Sum_probs=23.9
Q ss_pred CHHHHHHH-HhHHHHHHHHHHHHHHHhhhcC
Q psy6966 124 LVLETTIV-LGIEAVRKSVEKEMNTVLQFYG 153 (155)
Q Consensus 124 DI~EI~~V-LGIEAAR~aIIkEI~~Vf~~yG 153 (155)
|=.++++. +.=++||+.+..+++.++..+|
T Consensus 56 ~YD~LL~~g~~R~~AR~~V~~~~~~~L~~Wr 86 (86)
T PF10056_consen 56 DYDRLLREGYDRDEARRFVADRVNAVLREWR 86 (86)
T ss_pred cHHHHHHcCCCHHHHHHHHHHHHHHHHHhhC
Confidence 33466666 6679999999999999998765
No 42
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=23.35 E-value=70 Score=26.50 Aligned_cols=16 Identities=31% Similarity=0.324 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHh
Q psy6966 134 IEAVRKSVEKEMNTVL 149 (155)
Q Consensus 134 IEAAR~aIIkEI~~Vf 149 (155)
|||||.++.+-++...
T Consensus 62 iEAaR~a~~r~lkk~~ 77 (172)
T TIGR00279 62 LEAARIAANKYMTRRA 77 (172)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 7999999999888754
No 43
>KOG1914|consensus
Probab=23.32 E-value=59 Score=32.01 Aligned_cols=36 Identities=22% Similarity=0.074 Sum_probs=30.5
Q ss_pred eccccceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966 108 DPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEK 143 (155)
Q Consensus 108 eTeGt~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk 143 (155)
.-.+++.+|.+-+|||.+.-|.+.=|++|||....+
T Consensus 356 ~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~k 391 (656)
T KOG1914|consen 356 KLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKK 391 (656)
T ss_pred HHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHH
Confidence 334457899999999999999999999999986554
No 44
>PF03310 Cauli_DNA-bind: Caulimovirus DNA-binding protein; InterPro: IPR004986 The gene III product (P15) of cauliflower mosaic virus (CaMV) is a DNA binding protein in which the DNA binding activity is located on its C-terminal part. A family of related proteins is expressed by other members of the Caulimoviridae.; GO: 0003677 DNA binding; PDB: 3F6N_A 3K4T_D.
Probab=23.31 E-value=1.1e+02 Score=24.14 Aligned_cols=30 Identities=10% Similarity=0.159 Sum_probs=23.0
Q ss_pred eccCHHHHHHHH--------hHHHHHHHHHHHHHHHhh
Q psy6966 121 YHLLVLETTIVL--------GIEAVRKSVEKEMNTVLQ 150 (155)
Q Consensus 121 ySNDI~EI~~VL--------GIEAAR~aIIkEI~~Vf~ 150 (155)
...||.++++-+ .+||+-+.||+||...|+
T Consensus 18 ~~~~i~ailek~~s~~~~~e~lEsiAAKIIkDisdkId 55 (121)
T PF03310_consen 18 IESDIKAILEKLQSTEQDQENLESIAAKIIKDISDKID 55 (121)
T ss_dssp HHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHHH
Confidence 345666666554 499999999999998775
No 45
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=22.83 E-value=48 Score=23.42 Aligned_cols=20 Identities=20% Similarity=0.438 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHhhhcCC
Q psy6966 135 EAVRKSVEKEMNTVLQFYGL 154 (155)
Q Consensus 135 EAAR~aIIkEI~~Vf~~yGs 154 (155)
+++|...+.||+..|+.||.
T Consensus 19 ~~e~~~~~~~i~~~~~~~Gi 38 (93)
T PF00816_consen 19 KQEREEAIAEIRELMAEYGI 38 (93)
T ss_dssp HHCCHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHHHhCC
Confidence 45578899999999999995
No 46
>TIGR02482 PFKA_ATP 6-phosphofructokinase. 6-phosphofructokinase (EC 2.7.1.11) catalyzes the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This model hits bacterial ATP-dependent 6-phosphofructokinases which lack a beta-hairpin loop present in TIGR02483 family members. TIGR02483 contains members that are ATP-dependent as well as members that are pyrophosphate-dependent. TIGR02477 represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (EC 2.7.1.90).
Probab=22.75 E-value=54 Score=28.60 Aligned_cols=40 Identities=8% Similarity=-0.005 Sum_probs=34.7
Q ss_pred ccceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhh
Q psy6966 111 YGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQ 150 (155)
Q Consensus 111 Gt~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~ 150 (155)
|+.-|-.=+|..|||..+..++|-..|.+.+.+-|+++..
T Consensus 115 ~i~vigiPkTIDNDl~~td~s~GfdTA~~~~~~~i~~i~~ 154 (301)
T TIGR02482 115 GIPVIGLPGTIDNDIPGTDYTIGFDTALNTIIDAVDKIRD 154 (301)
T ss_pred CCCEEeecccccCCCcCcccCcChhHHHHHHHHHHHHHHH
Confidence 4556778899999999999999999999999998888754
No 47
>PF00015 MCPsignal: Methyl-accepting chemotaxis protein (MCP) signalling domain; InterPro: IPR004089 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the signalling domain found in several methyl-accepting chemotaxis proteins. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016020 membrane; PDB: 2CH7_A 3ZX6_B 1QU7_A 3G6B_B 3UR1_C 3G67_B.
Probab=22.36 E-value=88 Score=23.71 Aligned_cols=15 Identities=40% Similarity=0.539 Sum_probs=11.5
Q ss_pred hHHHHHH--------HHHHHHHH
Q psy6966 133 GIEAVRK--------SVEKEMNT 147 (155)
Q Consensus 133 GIEAAR~--------aIIkEI~~ 147 (155)
.|||||. .+-+||+.
T Consensus 64 sIEAaraGe~G~gF~vvA~eir~ 86 (213)
T PF00015_consen 64 SIEAARAGEAGRGFAVVADEIRK 86 (213)
T ss_dssp HHHHHHTCCCHHHHHHHHHHHHH
T ss_pred ccccchhcccchhHHHHHHHHHH
Confidence 4999996 67777765
No 48
>COG0332 FabH 3-oxoacyl-[acyl-carrier-protein]
Probab=22.29 E-value=1e+02 Score=27.47 Aligned_cols=38 Identities=29% Similarity=0.200 Sum_probs=27.3
Q ss_pred CccceEEeccccceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966 101 PEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEK 143 (155)
Q Consensus 101 ~~~e~~LeTeGt~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk 143 (155)
...+|+..--|+. .|-+..+ .|...-||+||||++|-+
T Consensus 29 tsdewI~~rtGir----~R~~a~~-~e~~s~la~~Aa~~AL~~ 66 (323)
T COG0332 29 TSDEWIETRTGIR----ERRIAAD-DETTSDLAVEAARKALED 66 (323)
T ss_pred CCcceeeeecCCc----eeeecCC-CccHHHHHHHHHHHHHHH
Confidence 4458998888872 1223333 788899999999999853
No 49
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=21.52 E-value=73 Score=25.81 Aligned_cols=14 Identities=29% Similarity=0.434 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHH
Q psy6966 134 IEAVRKSVEKEMNT 147 (155)
Q Consensus 134 IEAAR~aIIkEI~~ 147 (155)
|||||.++-+-++.
T Consensus 50 iEAARia~~R~lkr 63 (146)
T COG0197 50 IEAARIAANRYLKR 63 (146)
T ss_pred HHHHHHHHHHHhhh
Confidence 69999999887764
No 50
>PRK14510 putative bifunctional 4-alpha-glucanotransferase/glycogen debranching enzyme; Provisional
Probab=20.82 E-value=48 Score=34.27 Aligned_cols=19 Identities=47% Similarity=0.668 Sum_probs=15.4
Q ss_pred CCCCcccccCCC----CCCccccc
Q psy6966 1 MLPLHPLILPPS----SPYSCTST 20 (155)
Q Consensus 1 ~~~~~~~~~~~~----~~~~~~~~ 20 (155)
+|||||+- +-. ||||+.|.
T Consensus 765 ilPl~~~~-~~~p~~~SPYsp~S~ 787 (1221)
T PRK14510 765 VNPLHPLG-LGDPERASPYQPSSR 787 (1221)
T ss_pred ECCCCCCC-CCCCCCCCCccchhc
Confidence 58999975 556 99999885
No 51
>PRK04199 rpl10e 50S ribosomal protein L10e; Reviewed
Probab=20.60 E-value=81 Score=26.08 Aligned_cols=16 Identities=25% Similarity=0.403 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHh
Q psy6966 134 IEAVRKSVEKEMNTVL 149 (155)
Q Consensus 134 IEAAR~aIIkEI~~Vf 149 (155)
|||||.+|.+=++...
T Consensus 62 iEAaR~ai~r~lkk~~ 77 (172)
T PRK04199 62 LEAARIAANKYLTKTV 77 (172)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 6999999999888753
Done!