Query 003220
Match_columns 838
No_of_seqs 262 out of 761
Neff 2.9
Searched_HMMs 46136
Date Thu Mar 28 19:20:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003220hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 3.4E-26 7.4E-31 199.4 11.5 84 258-341 1-84 (84)
2 PRK10343 RNA-binding protein Y 99.9 6.1E-26 1.3E-30 204.9 12.8 88 257-344 2-89 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 8.7E-26 1.9E-30 202.9 12.8 88 258-345 1-88 (95)
4 COG1534 Predicted RNA-binding 99.9 3.8E-24 8.1E-29 193.5 12.1 88 257-344 1-88 (97)
5 TIGR00253 RNA_bind_YhbY putati 99.9 3.4E-24 7.5E-29 192.7 11.8 90 376-465 1-90 (95)
6 PRK10343 RNA-binding protein Y 99.9 4.2E-24 9E-29 193.0 11.6 88 375-462 2-89 (97)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 3.1E-24 6.7E-29 187.1 8.6 84 376-459 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 7.7E-23 1.7E-27 185.1 11.0 94 376-469 2-95 (97)
9 KOG1990 Poly(A)-specific exori 99.8 8.4E-19 1.8E-23 196.3 8.6 220 255-476 11-278 (564)
10 KOG1990 Poly(A)-specific exori 99.3 1.1E-11 2.4E-16 139.8 8.8 213 256-468 173-480 (564)
11 PRK06934 flavodoxin; Provision 45.7 46 0.00099 35.2 5.9 118 304-441 63-212 (221)
12 PF04472 DUF552: Protein of un 33.9 2.5E+02 0.0055 24.4 7.8 55 289-344 12-69 (73)
13 TIGR02630 xylose_isom_A xylose 33.1 12 0.00026 43.1 -0.5 27 186-212 52-79 (434)
14 PRK12465 xylose isomerase; Pro 29.1 28 0.0006 40.4 1.4 21 184-204 61-81 (445)
15 cd05796 Ribosomal_P0_like Ribo 27.6 48 0.001 33.0 2.6 67 373-441 25-98 (163)
16 cd03362 TOPRIM_TopoIA_TopoIII 27.1 3.1E+02 0.0068 26.6 7.9 80 328-415 42-124 (151)
17 PF04472 DUF552: Protein of un 26.7 2.5E+02 0.0053 24.5 6.5 51 407-458 12-65 (73)
18 PF01755 Glyco_transf_25: Glyc 26.1 65 0.0014 31.4 3.2 30 714-743 69-101 (200)
19 PF01918 Alba: Alba; InterPro 25.6 1.3E+02 0.0028 25.5 4.5 58 394-451 2-64 (70)
20 TIGR02565 cas_Csy2 CRISPR-asso 23.4 1.3E+02 0.0029 33.5 5.1 109 316-456 31-147 (296)
21 PF11272 DUF3072: Protein of u 23.1 47 0.001 29.2 1.4 18 374-391 14-31 (57)
22 KOG1924 RhoA GTPase effector D 22.2 5E+02 0.011 33.1 9.8 24 181-204 624-649 (1102)
23 PRK05474 xylose isomerase; Pro 22.2 42 0.00091 39.0 1.2 18 186-203 53-70 (437)
24 cd06532 Glyco_transf_25 Glycos 21.6 96 0.0021 29.1 3.2 31 713-743 65-98 (128)
25 PRK08173 DNA topoisomerase III 20.2 5.2E+02 0.011 32.5 9.8 92 328-424 37-132 (862)
No 1
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.93 E-value=3.4e-26 Score=199.37 Aligned_cols=84 Identities=29% Similarity=0.522 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCEE
Q 003220 258 LTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGVL 337 (838)
Q Consensus 258 LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~vI 337 (838)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||.+++..++++++++|+++|||++||+||+++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEc
Q 003220 338 YLFR 341 (838)
Q Consensus 338 VLYR 341 (838)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.93 E-value=6.1e-26 Score=204.87 Aligned_cols=88 Identities=20% Similarity=0.244 Sum_probs=86.4
Q ss_pred CCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCE
Q 003220 257 PLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGV 336 (838)
Q Consensus 257 ~LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~v 336 (838)
+||++|+++||++||+|+|+|+|||+|||++|+++|+++|++|||||||+++++.+++++++++|+++|||++||+||++
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~ 81 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKT 81 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcE
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCC
Q 003220 337 LYLFRGRN 344 (838)
Q Consensus 337 IVLYRGsN 344 (838)
+||||.+.
T Consensus 82 ~vlYR~~~ 89 (97)
T PRK10343 82 LVLYRPTK 89 (97)
T ss_pred EEEEecCC
Confidence 99999975
No 3
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.93 E-value=8.7e-26 Score=202.94 Aligned_cols=88 Identities=24% Similarity=0.313 Sum_probs=86.0
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCEE
Q 003220 258 LTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGVL 337 (838)
Q Consensus 258 LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~vI 337 (838)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++|||||||+++++.++.++++++|+++|||++||.||+++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~ 80 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccCCC
Q 003220 338 YLFRGRNY 345 (838)
Q Consensus 338 VLYRGsNY 345 (838)
||||++.-
T Consensus 81 vlYR~~~~ 88 (95)
T TIGR00253 81 VLYRPTKE 88 (95)
T ss_pred EEEecCCc
Confidence 99999753
No 4
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=3.8e-24 Score=193.52 Aligned_cols=88 Identities=26% Similarity=0.394 Sum_probs=85.5
Q ss_pred CCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCE
Q 003220 257 PLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGV 336 (838)
Q Consensus 257 ~LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~v 336 (838)
+||++|+++||++||+++|+|+|||+|||++|+++|+++|++||||||++.+++.+|++++++.|++++||.+||+||++
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~ 80 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT 80 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCC
Q 003220 337 LYLFRGRN 344 (838)
Q Consensus 337 IVLYRGsN 344 (838)
+||||.+.
T Consensus 81 ~vlyr~~~ 88 (97)
T COG1534 81 LVLYRESK 88 (97)
T ss_pred EEEEecCc
Confidence 99999443
No 5
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.91 E-value=3.4e-24 Score=192.67 Aligned_cols=90 Identities=22% Similarity=0.339 Sum_probs=87.5
Q ss_pred CCHHHHHHHHHcccCCCCcEecccCCcchHHHHHHHHHHhhCceEEEEecCCCCccHHHHHHHHHhhCCCEEEEEeCCEE
Q 003220 376 LTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFEREHI 455 (838)
Q Consensus 376 LTgKErtyLRslA~~L~PIfqLGKNGVt~gLV~qIreAwEkrELVKI~cLgn~~tD~keIAeELaeLTG~eLVQ~IGe~I 455 (838)
||+||++|||++||+|+|+++|||+|++++++.+|.+||++||||||.+++++..|.+++|++|++.|+|++||+||+++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~ 80 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCcC
Q 003220 456 LMWRGQEWKS 465 (838)
Q Consensus 456 VLYRGkdfkp 465 (838)
||||++...+
T Consensus 81 vlYR~~~~~~ 90 (95)
T TIGR00253 81 VLYRPTKERK 90 (95)
T ss_pred EEEecCCccC
Confidence 9999986544
No 6
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.91 E-value=4.2e-24 Score=193.01 Aligned_cols=88 Identities=15% Similarity=0.267 Sum_probs=86.5
Q ss_pred CCCHHHHHHHHHcccCCCCcEecccCCcchHHHHHHHHHHhhCceEEEEecCCCCccHHHHHHHHHhhCCCEEEEEeCCE
Q 003220 375 GLTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFEREH 454 (838)
Q Consensus 375 GLTgKErtyLRslA~~L~PIfqLGKNGVt~gLV~qIreAwEkrELVKI~cLgn~~tD~keIAeELaeLTG~eLVQ~IGe~ 454 (838)
.||+||++|||++||+|+|+|+|||+|++++++.+|.+||++||||||.+++++.++.+++|++|++.|+|++||+||++
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~ 81 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKT 81 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcE
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCC
Q 003220 455 ILMWRGQE 462 (838)
Q Consensus 455 IVLYRGkd 462 (838)
+||||.+.
T Consensus 82 ~vlYR~~~ 89 (97)
T PRK10343 82 LVLYRPTK 89 (97)
T ss_pred EEEEecCC
Confidence 99999985
No 7
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.90 E-value=3.1e-24 Score=187.15 Aligned_cols=84 Identities=26% Similarity=0.450 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHcccCCCCcEecccCCcchHHHHHHHHHHhhCceEEEEecCCCCccHHHHHHHHHhhCCCEEEEEeCCEE
Q 003220 376 LTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFEREHI 455 (838)
Q Consensus 376 LTgKErtyLRslA~~L~PIfqLGKNGVt~gLV~qIreAwEkrELVKI~cLgn~~tD~keIAeELaeLTG~eLVQ~IGe~I 455 (838)
||++|+++||++|++|+|+++|||+|+|++++++|+++|++||||||.|++++..+.+++|++|++.|||++||++|+++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEe
Q 003220 456 LMWR 459 (838)
Q Consensus 456 VLYR 459 (838)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 8
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=7.7e-23 Score=185.08 Aligned_cols=94 Identities=24% Similarity=0.372 Sum_probs=89.3
Q ss_pred CCHHHHHHHHHcccCCCCcEecccCCcchHHHHHHHHHHhhCceEEEEecCCCCccHHHHHHHHHhhCCCEEEEEeCCEE
Q 003220 376 LTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFEREHI 455 (838)
Q Consensus 376 LTgKErtyLRslA~~L~PIfqLGKNGVt~gLV~qIreAwEkrELVKI~cLgn~~tD~keIAeELaeLTG~eLVQ~IGe~I 455 (838)
||+||++|||++||++.|+|+|||||+++++++.|..+|++||||||.+++++..|.+++|++|++.+||++||+||+++
T Consensus 2 Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~ 81 (97)
T COG1534 2 LTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTL 81 (97)
T ss_pred CcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCcCCccC
Q 003220 456 LMWRGQEWKSSILK 469 (838)
Q Consensus 456 VLYRGkdfkp~y~~ 469 (838)
||||.+..+..+.-
T Consensus 82 vlyr~~~e~~~i~l 95 (97)
T COG1534 82 VLYRESKEKRKISL 95 (97)
T ss_pred EEEecCcccccccC
Confidence 99996665555543
No 9
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.76 E-value=8.4e-19 Score=196.30 Aligned_cols=220 Identities=22% Similarity=0.236 Sum_probs=201.1
Q ss_pred CCCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCC-EEEEEE
Q 003220 255 GEPLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGG-KIIYRR 333 (838)
Q Consensus 255 gE~LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGG-eVVQrI 333 (838)
+..+...+..+||..|..+.-.+ +++|+|+.+++.|++.|+.+|+++++|....+..|.+.++.++..|++ -+||+.
T Consensus 11 ~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~~~ 88 (564)
T KOG1990|consen 11 ELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVWSR 88 (564)
T ss_pred HhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeeeec
Confidence 34799999999999999998877 999999999999999999999999999999999999999999999999 999999
Q ss_pred CCEEEEEccCCCCCC-----------------------------CCCccccCCcCCC-----------CCCCCCCcccCC
Q 003220 334 GGVLYLFRGRNYNYR-----------------------------SRPRFPLMLWKPV-----------TPVYPRLIQQVP 373 (838)
Q Consensus 334 G~vIVLYRGsNY~~~-----------------------------~rPR~plmlwkP~-----------~P~Yp~l~r~lP 373 (838)
|.....|++..|..+ .+|++-+|+.... +|.|-+|++.+|
T Consensus 89 g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~ 168 (564)
T KOG1990|consen 89 GDSISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLP 168 (564)
T ss_pred CccccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCC
Confidence 999999976666543 2577777766432 688999999999
Q ss_pred CC----CCHHHHHHHHHcccCCCCcEecccCCcchHHHHHHHHHHhhCceEEEEe-cCCCCccHHHHHHHH--HhhCCCE
Q 003220 374 DG----LTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCELVRINC-QGMNGSDYRKIGAKL--RDLVPCV 446 (838)
Q Consensus 374 EG----LTgKErtyLRslA~~L~PIfqLGKNGVt~gLV~qIreAwEkrELVKI~c-Lgn~~tD~keIAeEL--aeLTG~e 446 (838)
.+ |+.+|+.++|.+|..++|||.+|.++..++++..|+..|++++.+||.| +|.+......+|.+| ..++|..
T Consensus 169 ~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~ 248 (564)
T KOG1990|consen 169 VGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKV 248 (564)
T ss_pred CCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCe
Confidence 88 9999999999999999999999999999999999999999999999999 699999999999999 9999999
Q ss_pred EEEEeCCEEEEEecCCCcCCccCCCCCchh
Q 003220 447 LISFEREHILMWRGQEWKSSILKPGNDSED 476 (838)
Q Consensus 447 LVQ~IGe~IVLYRGkdfkp~y~~~v~~~eE 476 (838)
||..++..+|+||+++|.+.-+....+++.
T Consensus 249 lv~hN~~~dv~y~~~~Fl~~lp~~l~~f~~ 278 (564)
T KOG1990|consen 249 LVLHNKLLDVMYRYKNFLSPLPSTLEEFTD 278 (564)
T ss_pred EEeeccceeeeeehhhcccccchhHHHhhh
Confidence 999999999999999999977777666665
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.25 E-value=1.1e-11 Score=139.76 Aligned_cols=213 Identities=21% Similarity=0.319 Sum_probs=177.2
Q ss_pred CCCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCC-hhhHHHHHHHH--HHHhCCEEEEE
Q 003220 256 EPLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVC-TVDMDNVCEQL--EERTGGKIIYR 332 (838)
Q Consensus 256 E~LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~-~eDmkeIaEeL--EekTGGeVVQr 332 (838)
..|+..+.-.+|.++..+.+.+.+|..+.-.++...+.+.|..|+..|+.+...- ......++.++ -..+|+.||.+
T Consensus 173 ~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~h 252 (564)
T KOG1990|consen 173 PLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLH 252 (564)
T ss_pred hhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEee
Confidence 3699999999999999999999999999999999999999999999998887644 33445777888 88999999999
Q ss_pred ECCEEEEEccCCCCCCC-------CC---ccccC-----------------------------Cc-CCC-----------
Q 003220 333 RGGVLYLFRGRNYNYRS-------RP---RFPLM-----------------------------LW-KPV----------- 361 (838)
Q Consensus 333 IG~vIVLYRGsNY~~~~-------rP---R~plm-----------------------------lw-kP~----------- 361 (838)
.+-..|+||+++|-.+. .. .||.+ -| +++
T Consensus 253 N~~~dv~y~~~~Fl~~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~ 332 (564)
T KOG1990|consen 253 NKLLDVMYRYKNFLSPLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRLKL 332 (564)
T ss_pred ccceeeeeehhhcccccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchhhh
Confidence 99999999998886531 01 11110 01 010
Q ss_pred ------------------------------------CCCCCCCcccCCCCCCHHHHHHHHHcccCCCCcEecccCCcchH
Q 003220 362 ------------------------------------TPVYPRLIQQVPDGLTLEEATEMRKKGRKLIPICKLGKNGVYCD 405 (838)
Q Consensus 362 ------------------------------------~P~Yp~l~r~lPEGLTgKErtyLRslA~~L~PIfqLGKNGVt~g 405 (838)
.+.-+..-+.+|+.+|.+++.++++.+..+....-+|+.|++.+
T Consensus 333 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g 412 (564)
T KOG1990|consen 333 EFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDG 412 (564)
T ss_pred hhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccc
Confidence 12233344488999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCceEEEEecCCC-CccHHHHHHHHHhhCCCEEEEEeCCE----EEEEecCCCcCCcc
Q 003220 406 LAKNVREAFEVCELVRINCQGMN-GSDYRKIGAKLRDLVPCVLISFEREH----ILMWRGQEWKSSIL 468 (838)
Q Consensus 406 LV~qIreAwEkrELVKI~cLgn~-~tD~keIAeELaeLTG~eLVQ~IGe~----IVLYRGkdfkp~y~ 468 (838)
++.+++.+|..+|++|+.|+.-. ....+..|..|....|+.+|+++... |+.|||++|.-...
T Consensus 413 ~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~ 480 (564)
T KOG1990|consen 413 VIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTS 480 (564)
T ss_pred eeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcc
Confidence 99999999999999999997554 49999999999999999999987533 89999999875433
No 11
>PRK06934 flavodoxin; Provisional
Probab=45.74 E-value=46 Score=35.21 Aligned_cols=118 Identities=14% Similarity=0.229 Sum_probs=0.0
Q ss_pred EEecCCChhhHHHHHHHHHHHhCCEEEEEECCEEEEEccCCCCCCC-----------CC-----------------cccc
Q 003220 304 IKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGVLYLFRGRNYNYRS-----------RP-----------------RFPL 355 (838)
Q Consensus 304 VK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~vIVLYRGsNY~~~~-----------rP-----------------R~pl 355 (838)
+...+...-+.+.+|++|++.+||.+... ...-.|-. +|+.-. +| -||.
T Consensus 63 ~~~~~~~~GnTk~vAe~Ia~~~gaDl~eI--~~~~~Y~~-~yd~~~~~a~~E~~~~~~P~L~~~~~dl~~YD~I~IG~PI 139 (221)
T PRK06934 63 LQKNGEVLGSTQYVAQIIQEETGGDLFRI--ETVKPYPR-QHDPLLKYAEQEVKEGGRPEMREKIQNLADYDQIFIGYPI 139 (221)
T ss_pred cccCCCCCCHHHHHHHHHHHHHCCCEEEE--EEccccCC-CCchhhhHHHHhhhcCCCHHHHHHHHhHHhCCEEEEEcch
Q ss_pred CCcCCCCCCCCCCcccCCCCCCHHHHHHHHH---cccCCCCcEecccCCcchHHHHHHHHHHhhC-ceEEEEecCCCCcc
Q 003220 356 MLWKPVTPVYPRLIQQVPDGLTLEEATEMRK---KGRKLIPICKLGKNGVYCDLAKNVREAFEVC-ELVRINCQGMNGSD 431 (838)
Q Consensus 356 mlwkP~~P~Yp~l~r~lPEGLTgKErtyLRs---lA~~L~PIfqLGKNGVt~gLV~qIreAwEkr-ELVKI~cLgn~~tD 431 (838)
|||.+..|+ ++||.+ .+.++-|+|.-|..| ..+-++.|+++..+. .+.+--........
T Consensus 140 Wwg~~P~~V----------------~tFLe~~d~~GK~I~pF~T~ggsg-~g~s~~~i~~l~~~a~~v~~Gl~i~~~~~~ 202 (221)
T PRK06934 140 WWYKMPMVM----------------YSFFEQHDFSGKTLIPFTTHGGSR-FSDSLREIKRLQPNAQLVTQGLAISRNDVT 202 (221)
T ss_pred hhccccHHH----------------HHHHHhcCCCCCEEEEEEecCCCC-ccchHHHHHHHcCCcceeccceeeecCccc
Q ss_pred HHHHHHHHHh
Q 003220 432 YRKIGAKLRD 441 (838)
Q Consensus 432 ~keIAeELae 441 (838)
..+..++|.+
T Consensus 203 ~~~~~~~I~~ 212 (221)
T PRK06934 203 DDDTPKEIIN 212 (221)
T ss_pred ccchHHHHHH
No 12
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=33.93 E-value=2.5e+02 Score=24.41 Aligned_cols=55 Identities=9% Similarity=0.157 Sum_probs=37.3
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCEEEEEECCEEEEEccCC
Q 003220 289 LDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEE---RTGGKIIYRRGGVLYLFRGRN 344 (838)
Q Consensus 289 VeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEe---kTGGeVVQrIG~vIVLYRGsN 344 (838)
+.+|-++++....|-+.+..-...+.+++.+.|.. ..+|.+.+. |..++|+=+.+
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i-~~~~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI-SEKVFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE-ETTEEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE-cCCEEEEECCC
Confidence 45688999999999999999888888988888875 678888776 55566665444
No 13
>TIGR02630 xylose_isom_A xylose isomerase. Members of this family are the enzyme xylose isomerase (5.3.1.5), which interconverts D-xylose and D-xylulose.
Probab=33.08 E-value=12 Score=43.08 Aligned_cols=27 Identities=41% Similarity=0.810 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCCCCCC-CCCCCCCccc
Q 003220 186 AAFSPFGPTTMGRPWTG-RAPLPPSKKK 212 (838)
Q Consensus 186 p~f~pfgp~~~~RpWtG-~~p~~~~k~~ 212 (838)
.---|||++|+.|||.+ ..|.-..|+|
T Consensus 52 ~G~DpFG~~T~~rpw~~~~d~~~~a~~k 79 (434)
T TIGR02630 52 DGGDPFGDGTADRPWDGGTDPMDKAKAK 79 (434)
T ss_pred CCCCCCCCccCCCCCccCCCHHHHHHHH
Confidence 34469999999999953 2344334443
No 14
>PRK12465 xylose isomerase; Provisional
Probab=29.10 E-value=28 Score=40.38 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=15.7
Q ss_pred ccCCCCCCCCCCCCCCCCCCC
Q 003220 184 REAAFSPFGPTTMGRPWTGRA 204 (838)
Q Consensus 184 rep~f~pfgp~~~~RpWtG~~ 204 (838)
+-+---|||++|+.|||.+-.
T Consensus 61 ~~~G~DpFG~~T~~rpw~~~~ 81 (445)
T PRK12465 61 CGNGADPFGPGTRAYPWDVGN 81 (445)
T ss_pred CCCCCCCCCCccCCCCcccCC
Confidence 334456999999999996543
No 15
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=27.64 E-value=48 Score=32.97 Aligned_cols=67 Identities=10% Similarity=0.081 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHcccCCCCcEecccCCcchHHHHHHHH------HHhhCceEEEEe-cCCCCccHHHHHHHHHh
Q 003220 373 PDGLTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVRE------AFEVCELVRINC-QGMNGSDYRKIGAKLRD 441 (838)
Q Consensus 373 PEGLTgKErtyLRslA~~L~PIfqLGKNGVt~gLV~qIre------AwEkrELVKI~c-Lgn~~tD~keIAeELae 441 (838)
=.+|+.+|.+.||+.-+.. .|.+|||.+..--+....+ .-+-.+.+|-.+ +=.+..|+.+++..|.+
T Consensus 25 ~~gl~~~ql~~iR~~lr~~--~~~v~KNtl~~~Al~~~~~~~~~~~~~~L~~~l~G~~~lift~~dp~~v~k~l~~ 98 (163)
T cd05796 25 VDNMRNNKLKDIRQEWKDS--RFFFGKNKVMQVALGRTPEDEYKPNLHKLSKYLKGQVGLLFTNEPPEEVIEYFDS 98 (163)
T ss_pred ecCCCHHHHHHHHHHhcCC--EEEEEchHHHHHHHhhCccccccccHHHHHHHhCCCEEEEEECCCHHHHHHHHHH
Confidence 3679999999999987764 7888999875443332211 111122333333 22344566666666665
No 16
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=27.08 E-value=3.1e+02 Score=26.65 Aligned_cols=80 Identities=15% Similarity=0.207 Sum_probs=39.6
Q ss_pred EEEEEECCEEEEEccCCCCCCCCCccccCCcCCCCCCCCCCcccCCCCCCHHHHHHHHHcccCCCCcEec---ccCCcch
Q 003220 328 KIIYRRGGVLYLFRGRNYNYRSRPRFPLMLWKPVTPVYPRLIQQVPDGLTLEEATEMRKKGRKLIPICKL---GKNGVYC 404 (838)
Q Consensus 328 eVVQrIG~vIVLYRGsNY~~~~rPR~plmlwkP~~P~Yp~l~r~lPEGLTgKErtyLRslA~~L~PIfqL---GKNGVt~ 404 (838)
.|++..||.+=|.-...|. +.+..|.+.. |.++..++..+..-+.++...|+++++.-.-++.- +|.| +
T Consensus 42 ~vt~~~GHl~~l~~p~~y~----~~~~~~~~~~--p~~~~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEG--E 113 (151)
T cd03362 42 VVTWASGHLLELDFPEEYD----PWDKVWPLED--PLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREG--E 113 (151)
T ss_pred EEEEEhhHhhcccChHHhc----cCCCCCcccc--CCcCCceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccc--c
Confidence 5777888877665555553 2222221111 33433333333334566777777777665544443 3444 2
Q ss_pred HHHHHHHHHHh
Q 003220 405 DLAKNVREAFE 415 (838)
Q Consensus 405 gLV~qIreAwE 415 (838)
.+...|.+.+.
T Consensus 114 ~I~~~i~~~~~ 124 (151)
T cd03362 114 LIGREILEYAK 124 (151)
T ss_pred HHHHHHHHHhC
Confidence 33334555554
No 17
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=26.71 E-value=2.5e+02 Score=24.51 Aligned_cols=51 Identities=12% Similarity=0.257 Sum_probs=37.5
Q ss_pred HHHHHHHHhhCceEEEEecCCCCccHHHHHHHHHh---hCCCEEEEEeCCEEEEE
Q 003220 407 AKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRD---LVPCVLISFEREHILMW 458 (838)
Q Consensus 407 V~qIreAwEkrELVKI~cLgn~~tD~keIAeELae---LTG~eLVQ~IGe~IVLY 458 (838)
+..|.+++....+|=+++......+.+++.+.|+- ..+|.+..+-.+ ++|+
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i~~~-~~l~ 65 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKISEK-VFLL 65 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEEETT-EEEE
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEEcCC-EEEE
Confidence 34588999999999999999999999999999987 569998888555 4444
No 18
>PF01755 Glyco_transf_25: Glycosyltransferase family 25 (LPS biosynthesis protein); InterPro: IPR002654 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 25 GT25 from CAZY comprises enzymes with only one known activity; as a lipopolysaccharide biosynthesis protein. These enzymes catalyse the transfer of various sugars onto the growing lipopolysaccharide chain during its biosynthesis [].; GO: 0009103 lipopolysaccharide biosynthetic process
Probab=26.07 E-value=65 Score=31.43 Aligned_cols=30 Identities=30% Similarity=0.444 Sum_probs=21.8
Q ss_pred chHHHHHHHHHHHHhcC--CeEEe-cCCCCCch
Q 003220 714 PSLEIVLHLMRQAVENG--SALVL-DDATLDAD 743 (838)
Q Consensus 714 ~~~~~~l~l~~qave~g--~alvl-d~~~~dad 743 (838)
-|.--=+.+|+++|++| -|||| ||..++.|
T Consensus 69 GC~lSH~~~w~~~v~~~~~~~lIlEDDv~~~~~ 101 (200)
T PF01755_consen 69 GCALSHIKAWQRIVDSGLEYALILEDDVIFDPD 101 (200)
T ss_pred eehhhHHHHHHHHHHcCCCeEEEEecccccccc
Confidence 34555578999999999 78999 55555544
No 19
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function. The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
Probab=25.63 E-value=1.3e+02 Score=25.53 Aligned_cols=58 Identities=12% Similarity=0.005 Sum_probs=49.0
Q ss_pred cEecccCCcchHHHHHHHHHH-----hhCceEEEEecCCCCccHHHHHHHHHhhCCCEEEEEe
Q 003220 394 ICKLGKNGVYCDLAKNVREAF-----EVCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFE 451 (838)
Q Consensus 394 IfqLGKNGVt~gLV~qIreAw-----EkrELVKI~cLgn~~tD~keIAeELaeLTG~eLVQ~I 451 (838)
.+.|+++.-....+..+..+| ...+-|.|.-+|..-.-.=.+|+.|++..+..++|+.
T Consensus 2 ~I~V~~~~~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv~ 64 (70)
T PF01918_consen 2 EIYVSSNSPIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQVN 64 (70)
T ss_dssp EEEE-STS-HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEEE
T ss_pred EEEECCCCCHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEEE
Confidence 467899999999999999999 9999999999999999999999999998865555543
No 20
>TIGR02565 cas_Csy2 CRISPR-associated protein, Csy2 family. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2464 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy2, for CRISPR/Cas Subtype Ypest protein 2.
Probab=23.37 E-value=1.3e+02 Score=33.48 Aligned_cols=109 Identities=16% Similarity=0.202 Sum_probs=72.4
Q ss_pred HHHHHHHHHhCCEEEEEECCEEEEEccCCCCCCCCCccccCCcCCCCCCCCCCcccCCCCCCHHHHHHHHHcccCCCCcE
Q 003220 316 NVCEQLEERTGGKIIYRRGGVLYLFRGRNYNYRSRPRFPLMLWKPVTPVYPRLIQQVPDGLTLEEATEMRKKGRKLIPIC 395 (838)
Q Consensus 316 eIaEeLEekTGGeVVQrIG~vIVLYRGsNY~~~~rPR~plmlwkP~~P~Yp~l~r~lPEGLTgKErtyLRslA~~L~PIf 395 (838)
-+...|+++++..+.-.+.++.|+-++-.++. .++. ++|..-|.. | -.|
T Consensus 31 Gf~HaL~RkL~~~~~~~~~~~~v~~H~~~~q~----------~~~~-~~~~~~f~~-----t-------------rnp-- 79 (296)
T TIGR02565 31 GFMHALSRKLGASHGLTLHGVGVACHGQQLHT----------YGSA-QRWDRVFIL-----T-------------RNP-- 79 (296)
T ss_pred HHHHHHHHHhCCCCCeEEeeEEEEECCccccc----------ccCC-CCccceeec-----c-------------cCc--
Confidence 45667788887766556778888888777762 2221 333222222 1 122
Q ss_pred ecccCCcchHHHHHHHHHHhhCceEEEEe-c-CCCCccHHHHHHHHHh------hCCCEEEEEeCCEEE
Q 003220 396 KLGKNGVYCDLAKNVREAFEVCELVRINC-Q-GMNGSDYRKIGAKLRD------LVPCVLISFEREHIL 456 (838)
Q Consensus 396 qLGKNGVt~gLV~qIreAwEkrELVKI~c-L-gn~~tD~keIAeELae------LTG~eLVQ~IGe~IV 456 (838)
+.|+|-+..++..-+-+++-+-||+++- . .+...+.+++++.|.+ +.||.|+.+++...|
T Consensus 80 -l~k~g~t~~i~ee~r~HL~vSLvI~~~g~~~~~~~~~~~~~~~~~~~~l~~~RlAGG~Il~~~~~~~i 147 (296)
T TIGR02565 80 -VTKNGKTAAIIEEGRCHLTVSLVIGVSGSDIAPTDDALQALLEHLKQLLKQQRLAGGTVIEFIERVQV 147 (296)
T ss_pred -cccCCCCCccCccceeeeEEEEEEEEcccccCCcchhHHHHHHHHHHHHHhCcccCceecCCcCccee
Confidence 2579999999999999999999999996 2 2234566777777776 568888887444433
No 21
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=23.11 E-value=47 Score=29.17 Aligned_cols=18 Identities=11% Similarity=0.172 Sum_probs=15.3
Q ss_pred CCCCHHHHHHHHHcccCC
Q 003220 374 DGLTLEEATEMRKKGRKL 391 (838)
Q Consensus 374 EGLTgKErtyLRslA~~L 391 (838)
+.||+.|+.|||.|+..-
T Consensus 14 ePmT~aQ~syL~tL~e~A 31 (57)
T PF11272_consen 14 EPMTGAQASYLKTLSEEA 31 (57)
T ss_pred CCCcHHHHHHHHHHHHHh
Confidence 459999999999998754
No 22
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=22.20 E-value=5e+02 Score=33.10 Aligned_cols=24 Identities=17% Similarity=0.422 Sum_probs=15.1
Q ss_pred cccccCCCCCCCCCCCCCC--CCCCC
Q 003220 181 LKLREAAFSPFGPTTMGRP--WTGRA 204 (838)
Q Consensus 181 i~~rep~f~pfgp~~~~Rp--WtG~~ 204 (838)
+.+|-+.|+-.-|.-|.+. |++..
T Consensus 624 ~~Mrr~nW~kI~p~d~s~~cFWvkv~ 649 (1102)
T KOG1924|consen 624 VPMRRFNWSKIVPRDLSENCFWVKVN 649 (1102)
T ss_pred CccccCCccccCccccCccceeeecc
Confidence 4566666666666666664 66654
No 23
>PRK05474 xylose isomerase; Provisional
Probab=22.20 E-value=42 Score=38.99 Aligned_cols=18 Identities=39% Similarity=0.837 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 003220 186 AAFSPFGPTTMGRPWTGR 203 (838)
Q Consensus 186 p~f~pfgp~~~~RpWtG~ 203 (838)
+---|||++|+.|||...
T Consensus 53 ~G~DpFG~~T~~rpw~~~ 70 (437)
T PRK05474 53 PGADPFGGGTFQRPWDQP 70 (437)
T ss_pred CCCCCCCCccccCCCcCC
Confidence 344699999999999744
No 24
>cd06532 Glyco_transf_25 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of Neisseria gonorrhoeae and Lic2A of Haemophilus influenzae. M. catarrhalis Lgt2 catalyzes the addition of galactose (Gal) to the growing chain of LOS on the cell surface. N. gonorrhoeae LgtB and LgtE link Gal-beta(1,4) to GlcNAc (N-acetylglucosamine) and Glc (glucose), respectively. The genes encoding LgtB and LgtE are two genes of a five gene locus involved in the synthesis of gonococcal LOS. LgtE is believed to perform the first step in LOS biosynthesis.
Probab=21.56 E-value=96 Score=29.06 Aligned_cols=31 Identities=32% Similarity=0.381 Sum_probs=22.3
Q ss_pred CchHHHHHHHHHHHHhcC--CeEEecCC-CCCch
Q 003220 713 GPSLEIVLHLMRQAVENG--SALVLDDA-TLDAD 743 (838)
Q Consensus 713 ~~~~~~~l~l~~qave~g--~alvld~~-~~dad 743 (838)
--|.-.=+.+|+++|++| .||||||| .++.|
T Consensus 65 iGC~lSH~~~w~~~~~~~~~~alIlEDDv~~~~~ 98 (128)
T cd06532 65 IGCFLSHYKLWQKIVESNLEYALILEDDAILDPD 98 (128)
T ss_pred HHHHHHHHHHHHHHHHcCCCeEEEEccCcEECCC
Confidence 345556678999999998 68888555 45555
No 25
>PRK08173 DNA topoisomerase III; Validated
Probab=20.25 E-value=5.2e+02 Score=32.52 Aligned_cols=92 Identities=13% Similarity=0.091 Sum_probs=60.4
Q ss_pred EEEEEECCEEEEEccCCCCCCCCCccccCCcCCCCCCCCCCcccCCCCCCHHHHHHHHHcccC--CCCcEecccCCcchH
Q 003220 328 KIIYRRGGVLYLFRGRNYNYRSRPRFPLMLWKPVTPVYPRLIQQVPDGLTLEEATEMRKKGRK--LIPICKLGKNGVYCD 405 (838)
Q Consensus 328 eVVQrIG~vIVLYRGsNY~~~~rPR~plmlwkP~~P~Yp~l~r~lPEGLTgKErtyLRslA~~--L~PIfqLGKNGVt~g 405 (838)
.|.|.+||.+=|.=+..|+ |.|..|-. -..|++|..|+..|-.=+.+|...|+++.+. ..=|+.-+-.|-=.+
T Consensus 37 ~Vtwa~GHL~el~~Pe~Y~----~~~~~W~~-~~LPi~p~~f~~~~~~~~~~q~~~ik~l~k~~~~d~Ii~AtD~dREGE 111 (862)
T PRK08173 37 VLSSAVGHLLEIAAPEEYE----VKRGKWSF-AHLPVIPPHFDLNPIAKTESRLKVLTKLIKRKDVTRLINACDAGREGE 111 (862)
T ss_pred EEEeeccccccCCCchhcc----cccccccc-cccCCCCccccccccccHHHHHHHHHHHHhhCCCCEEEECCCCChhHH
Confidence 5779999999998777774 56654432 2347788777765544477899999999854 555777665555555
Q ss_pred HHHH-HHHHHhhC-ceEEEEe
Q 003220 406 LAKN-VREAFEVC-ELVRINC 424 (838)
Q Consensus 406 LV~q-IreAwEkr-ELVKI~c 424 (838)
+|-. |.+++... .+-++-+
T Consensus 112 lI~~~I~~~~~~~kpv~Rlw~ 132 (862)
T PRK08173 112 LIFRLIAQHAKAKKPVKRLWL 132 (862)
T ss_pred HHHHHHHHHhCCCCCeEEEEE
Confidence 5554 66666532 3334444
Done!