Query 014482
Match_columns 423
No_of_seqs 248 out of 813
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:34:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014482.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014482hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10343 RNA-binding protein Y 100.0 6.7E-28 1.5E-32 204.1 12.6 89 167-257 1-89 (97)
2 PRK10343 RNA-binding protein Y 99.9 1.1E-27 2.3E-32 202.9 11.3 89 288-376 2-90 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 1.6E-27 3.5E-32 200.9 11.4 90 289-378 1-90 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.9E-27 4.1E-32 194.9 11.3 84 169-254 1-84 (84)
5 TIGR00253 RNA_bind_YhbY putati 99.9 3.6E-27 7.7E-32 198.9 12.4 87 169-257 1-87 (95)
6 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.1E-26 2.3E-31 190.5 8.6 84 289-372 1-84 (84)
7 COG1534 Predicted RNA-binding 99.9 7.9E-26 1.7E-30 191.4 11.8 87 168-256 1-87 (97)
8 COG1534 Predicted RNA-binding 99.9 6E-26 1.3E-30 192.2 10.6 91 288-378 1-91 (97)
9 KOG1990 Poly(A)-specific exori 99.7 1.3E-16 2.8E-21 169.3 8.4 220 166-391 11-278 (564)
10 KOG1990 Poly(A)-specific exori 99.1 1.1E-10 2.3E-15 124.5 7.0 213 167-381 173-480 (564)
11 PF04472 DUF552: Protein of un 54.1 89 0.0019 25.0 7.6 55 202-257 12-69 (73)
12 PF04472 DUF552: Protein of un 53.4 65 0.0014 25.8 6.7 53 316-369 9-64 (73)
13 PRK12465 xylose isomerase; Pro 36.4 18 0.00038 39.0 1.3 19 114-132 62-80 (445)
14 PF01918 Alba: Alba; InterPro 34.6 1.1E+02 0.0024 23.8 5.3 58 307-364 2-64 (70)
15 cd05796 Ribosomal_P0_like Ribo 34.1 30 0.00064 31.9 2.2 67 286-354 25-98 (163)
16 PF11272 DUF3072: Protein of u 34.1 27 0.00058 28.0 1.7 21 284-304 11-31 (57)
17 PF10369 ALS_ss_C: Small subun 31.5 1.1E+02 0.0023 24.9 4.8 39 212-252 2-40 (75)
18 PRK05474 xylose isomerase; Pro 30.6 24 0.00052 38.1 1.1 16 117-132 55-70 (437)
19 TIGR00730 conserved hypothetic 29.2 1.7E+02 0.0037 27.4 6.5 57 297-354 119-177 (178)
20 TIGR02630 xylose_isom_A xylose 28.9 27 0.00059 37.6 1.2 15 117-131 54-68 (434)
21 PTZ00135 60S acidic ribosomal 26.9 1.2E+02 0.0026 31.1 5.4 78 172-254 12-91 (310)
22 COG1098 VacB Predicted RNA bin 26.3 53 0.0011 30.2 2.4 28 197-224 38-65 (129)
23 cd08619 PI-PLCXDc_plant Cataly 26.1 1.2E+02 0.0026 31.1 5.1 63 198-260 93-171 (285)
24 cd02810 DHOD_DHPD_FMN Dihydroo 25.4 6.3E+02 0.014 24.5 11.0 113 199-366 83-198 (289)
25 PF11608 Limkain-b1: Limkain b 25.1 65 0.0014 28.0 2.6 26 227-252 19-44 (90)
26 cd03362 TOPRIM_TopoIA_TopoIII 24.0 5E+02 0.011 23.3 8.2 82 241-328 42-124 (151)
27 PRK10550 tRNA-dihydrouridine s 23.6 4.7E+02 0.01 26.6 8.9 40 318-363 184-223 (312)
28 PF04019 DUF359: Protein of un 23.4 2.1E+02 0.0046 25.7 5.6 49 194-244 43-91 (121)
29 cd05795 Ribosomal_P0_L10e Ribo 22.6 60 0.0013 30.2 2.1 68 286-354 25-97 (175)
30 PF03641 Lysine_decarbox: Poss 22.4 1.1E+02 0.0023 27.0 3.6 35 296-330 75-110 (133)
31 KOG1136 Predicted cleavage and 22.0 2.2E+02 0.0047 30.7 6.1 88 237-332 158-261 (501)
32 cd04734 OYE_like_3_FMN Old yel 20.8 5.7E+02 0.012 26.2 8.9 48 200-248 196-251 (343)
33 cd02933 OYE_like_FMN Old yello 20.8 7.2E+02 0.016 25.5 9.6 47 199-247 206-262 (338)
34 PF01221 Dynein_light: Dynein 20.4 2.5E+02 0.0055 23.1 5.2 26 317-354 19-44 (89)
35 cd05795 Ribosomal_P0_L10e Ribo 20.2 1.6E+02 0.0034 27.5 4.3 47 172-222 5-51 (175)
36 cd02931 ER_like_FMN Enoate red 20.1 5.7E+02 0.012 26.6 8.8 49 200-249 206-275 (382)
No 1
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.95 E-value=6.7e-28 Score=204.08 Aligned_cols=89 Identities=25% Similarity=0.298 Sum_probs=86.9
Q ss_pred CCCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEE
Q 014482 167 EPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRH 246 (423)
Q Consensus 167 e~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~I 246 (423)
|+||++|+++||++|| +|+|+|+|||+|||++|+++|+++|++|||||||+++++.++.++++++|+++|||++||+|
T Consensus 1 m~Lt~kqr~~LR~~ah--~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~I 78 (97)
T PRK10343 1 MNLSTKQKQHLKGLAH--PLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI 78 (97)
T ss_pred CCCCHHHHHHHHHhcC--CCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee
Confidence 5799999999999998 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccEEEEeccCC
Q 014482 247 GGTLVLYRGRN 257 (423)
Q Consensus 247 G~viVLYRg~n 257 (423)
|+++||||++.
T Consensus 79 G~~~vlYR~~~ 89 (97)
T PRK10343 79 GKTLVLYRPTK 89 (97)
T ss_pred CcEEEEEecCC
Confidence 99999999974
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.95 E-value=1.1e-27 Score=202.86 Aligned_cols=89 Identities=15% Similarity=0.184 Sum_probs=87.2
Q ss_pred CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482 288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ 367 (423)
Q Consensus 288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~ 367 (423)
+||+||++|||++||+|+|+|+|||+|++++++++|++||++||||||+|++++.+|.+++|++|++.|||++||+||++
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 EEEEcCCCC
Q 014482 368 IVVWRGKDY 376 (423)
Q Consensus 368 IVLYRgk~~ 376 (423)
+||||.++.
T Consensus 82 ~vlYR~~~~ 90 (97)
T PRK10343 82 LVLYRPTKE 90 (97)
T ss_pred EEEEecCCC
Confidence 999999863
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=99.95 E-value=1.6e-27 Score=200.93 Aligned_cols=90 Identities=18% Similarity=0.254 Sum_probs=87.6
Q ss_pred CCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCEE
Q 014482 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQI 368 (423)
Q Consensus 289 LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~I 368 (423)
||+||++|||++||+|+|+++|||+|++++++++|++||++||||||++++++.+|.+++|++|++.|||++||+||+++
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 EEEcCCCCCC
Q 014482 369 VVWRGKDYKH 378 (423)
Q Consensus 369 VLYRgk~~~p 378 (423)
||||++++.+
T Consensus 81 vlYR~~~~~~ 90 (95)
T TIGR00253 81 VLYRPTKERK 90 (95)
T ss_pred EEEecCCccC
Confidence 9999987543
No 4
>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=99.95 E-value=1.9e-27 Score=194.92 Aligned_cols=84 Identities=36% Similarity=0.543 Sum_probs=75.4
Q ss_pred CCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEcc
Q 014482 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGG 248 (423)
Q Consensus 169 LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG~ 248 (423)
||++|+++||++|| +++|+|+|||+|||++|+++|+++|++||||||||.+++.++++++|++|+++|||++||++|+
T Consensus 1 Lt~ke~~~Lr~~a~--~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~ 78 (84)
T PF01985_consen 1 LTSKERKFLRKLAH--HLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGR 78 (84)
T ss_dssp --HHHHHHHHHHHT--TC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETT
T ss_pred CCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECC
Confidence 79999999999998 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEec
Q 014482 249 TLVLYR 254 (423)
Q Consensus 249 viVLYR 254 (423)
++||||
T Consensus 79 ~~vlyR 84 (84)
T PF01985_consen 79 TIVLYR 84 (84)
T ss_dssp EEEEEE
T ss_pred EEEEEC
Confidence 999998
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=99.95 E-value=3.6e-27 Score=198.89 Aligned_cols=87 Identities=26% Similarity=0.379 Sum_probs=85.2
Q ss_pred CCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEcc
Q 014482 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGG 248 (423)
Q Consensus 169 LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG~ 248 (423)
||++|+++||++|| +|+|+|+|||+|||++|+++|+++|++||||||++++++.++.++++++|+++|||++||+||+
T Consensus 1 Lt~kqr~~Lr~~ah--~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~ 78 (95)
T TIGR00253 1 LTGKQKRHLRGKAH--HLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGK 78 (95)
T ss_pred CCHHHHHHHHHHhC--CCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEcc
Confidence 79999999999998 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeccCC
Q 014482 249 TLVLYRGRN 257 (423)
Q Consensus 249 viVLYRg~n 257 (423)
++||||++.
T Consensus 79 ~~vlYR~~~ 87 (95)
T TIGR00253 79 TIVLYRPTK 87 (95)
T ss_pred EEEEEecCC
Confidence 999999963
No 6
>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=99.94 E-value=1.1e-26 Score=190.50 Aligned_cols=84 Identities=27% Similarity=0.372 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCEE
Q 014482 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQI 368 (423)
Q Consensus 289 LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~I 368 (423)
||++|+++||++|++|+|+++|||+|+|++++++|+++|++||||||+|++++..|.+++|++|++.|||++||++|+++
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 014482 369 VVWR 372 (423)
Q Consensus 369 VLYR 372 (423)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 7
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=7.9e-26 Score=191.41 Aligned_cols=87 Identities=29% Similarity=0.463 Sum_probs=84.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482 168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG 247 (423)
Q Consensus 168 ~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG 247 (423)
+||++|+++||+.|| +++|+|+|||+|||++|+.+|+++|++||||||++++++.+|.+++|+.|++.+||++||+||
T Consensus 1 ~Lt~kq~~~Lrs~Ah--~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG 78 (97)
T COG1534 1 MLTGKQKRFLRSKAH--HLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIG 78 (97)
T ss_pred CCcHHHHHHHHHhhc--cCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeee
Confidence 589999999999998 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEeccC
Q 014482 248 GTLVLYRGR 256 (423)
Q Consensus 248 ~viVLYRg~ 256 (423)
+++||||.+
T Consensus 79 ~~~vlyr~~ 87 (97)
T COG1534 79 KTLVLYRES 87 (97)
T ss_pred eEEEEEecC
Confidence 999999943
No 8
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=6e-26 Score=192.16 Aligned_cols=91 Identities=20% Similarity=0.289 Sum_probs=87.8
Q ss_pred CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482 288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ 367 (423)
Q Consensus 288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~ 367 (423)
+||+||+++||++||++.|+|+|||||++++++++|+++|++||||||++++++..|.+++|++|++.+||++||+||++
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 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcCCCCCC
Q 014482 368 IVVWRGKDYKH 378 (423)
Q Consensus 368 IVLYRgk~~~p 378 (423)
+||||.+.++.
T Consensus 81 ~vlyr~~~e~~ 91 (97)
T COG1534 81 LVLYRESKEKR 91 (97)
T ss_pred EEEEecCcccc
Confidence 99999665553
No 9
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.66 E-value=1.3e-16 Score=169.32 Aligned_cols=220 Identities=19% Similarity=0.142 Sum_probs=194.3
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCC-eEEE
Q 014482 166 GEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG-KIIF 244 (423)
Q Consensus 166 ~e~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTgg-eVVq 244 (423)
.+.+...+..+||..|- .+.-.+ +++|+|+++++.|++.|+.+|+++++|....+..|....+.++..|++ -+||
T Consensus 11 ~~~~~~~~~~~l~~~~~--~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~ 86 (564)
T KOG1990|consen 11 ELTVDEADLRRLRLVAT--GMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVW 86 (564)
T ss_pred HhhcCHHHHHHHhhhhc--cceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeee
Confidence 45688999999999995 666555 999999999999999999999999999999999999999999999999 9999
Q ss_pred EEccEEEEeccCCCCCC----CCC---c--------------------ccccccCC--CCCCCcCcccccC---------
Q 014482 245 RHGGTLVLYRGRNYNPK----KRP---V--------------------IPLMLWRP--HEPVYPKLIKTTI--------- 286 (423)
Q Consensus 245 ~IG~viVLYRg~nY~p~----~Rp---k--------------------IpLm~Wk~--~~Pv~p~ll~~~~--------- 286 (423)
+.|-....|++..|.-+ .|- . -.+++|+. ..|++.++++.++
T Consensus 87 ~~g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~ 166 (564)
T KOG1990|consen 87 SRGDSISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRT 166 (564)
T ss_pred ecCccccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhcc
Confidence 99999988866665421 111 1 12369994 4899999987754
Q ss_pred ------CCCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEe-cCCCcccHHHHHHHH--HhhcC
Q 014482 287 ------EGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDC-QGLERSDYKKIGCKL--RDLVP 357 (423)
Q Consensus 287 ------e~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~v-l~n~~~D~keia~eL--aelTg 357 (423)
..||.++..++|.+|..++|+|.+|.++..++++..+...|++++++|+.| ++.+......+|.++ ...+|
T Consensus 167 l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg 246 (564)
T KOG1990|consen 167 LPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTG 246 (564)
T ss_pred CCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcC
Confidence 499999999999999999999999999999999999999999999999998 788999999999999 99999
Q ss_pred CEEEEEeCCEEEEEcCCCCCCCCCCcccchhccc
Q 014482 358 CILVTFEKEQIVVWRGKDYKHPGDDGQFFTHREL 391 (423)
Q Consensus 358 ~~lVq~iG~~IVLYRgk~~~p~~v~~~~~~ere~ 391 (423)
..||..++..+|+||+++|.+ .+ .+.+.+++.
T Consensus 247 ~~lv~hN~~~dv~y~~~~Fl~-~l-p~~l~~f~~ 278 (564)
T KOG1990|consen 247 KVLVLHNKLLDVMYRYKNFLS-PL-PSTLEEFTD 278 (564)
T ss_pred CeEEeeccceeeeeehhhccc-cc-chhHHHhhh
Confidence 999999999999999999999 77 777777776
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.10 E-value=1.1e-10 Score=124.55 Aligned_cols=213 Identities=21% Similarity=0.272 Sum_probs=174.4
Q ss_pred CCCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChH-hHHHHHHHH--HHhhCCeEE
Q 014482 167 EPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTV-DMKNVCFQL--EDKTFGKII 243 (423)
Q Consensus 167 e~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~-dmkeiae~L--eekTggeVV 243 (423)
..|+..+.-.+|.++. .+.+.+.+|.++.-.++...+...|+.|+.+|+.|...-.. ....++..+ -..+|+.||
T Consensus 173 ~~l~~~~~~~~r~~~~--~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv 250 (564)
T KOG1990|consen 173 PLLTSIESTLLRRLGY--KLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLV 250 (564)
T ss_pred hhhhhHHHHHHHHhcc--cccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEE
Confidence 5699999999999997 89999999999999999999999999999999888854443 444677777 889999999
Q ss_pred EEEccEEEEeccCCCCCC--------CC-----Ccccc--------------------------cccCCC----------
Q 014482 244 FRHGGTLVLYRGRNYNPK--------KR-----PVIPL--------------------------MLWRPH---------- 274 (423)
Q Consensus 244 q~IG~viVLYRg~nY~p~--------~R-----pkIpL--------------------------m~Wk~~---------- 274 (423)
.+.+-..|+||+++|-.+ ++ |.+.. -.|...
T Consensus 251 ~hN~~~dv~y~~~~Fl~~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~ 330 (564)
T KOG1990|consen 251 LHNKLLDVMYRYKNFLSPLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRL 330 (564)
T ss_pred eeccceeeeeehhhcccccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchh
Confidence 999999999998887541 11 11100 012110
Q ss_pred --------------------------------------CCCCcCcccccCCCCCHHHHHHHHHcCCCCCceEEeccCCch
Q 014482 275 --------------------------------------EPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYY 316 (423)
Q Consensus 275 --------------------------------------~Pv~p~ll~~~~e~LT~KQr~yLR~lA~~l~PifqLGKnGv~ 316 (423)
.+--+-.....++.+|.+++.+++++|..+....-+|+.|+.
T Consensus 331 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f 410 (564)
T KOG1990|consen 331 KLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVF 410 (564)
T ss_pred hhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccc
Confidence 000011122456799999999999999999999999999999
Q ss_pred hhHHHHHHHHHhcCceEEEEecCCCc-ccHHHHHHHHHhhcCCEEEEEeCC-E---EEEEcCCCCCCCCC
Q 014482 317 GSLVPMVRDAFLVSELVRIDCQGLER-SDYKKIGCKLRDLVPCILVTFEKE-Q---IVVWRGKDYKHPGD 381 (423)
Q Consensus 317 ~~Lv~~V~eAlEkrELVKI~vl~n~~-~D~keia~eLaelTg~~lVq~iG~-~---IVLYRgk~~~p~~v 381 (423)
.+++.+.+.+|..+|++|+.|+.-.. ...++.|..+....|..+|+++.. . |+.||+++|.-+..
T Consensus 411 ~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~ 480 (564)
T KOG1990|consen 411 DGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTS 480 (564)
T ss_pred cceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcc
Confidence 99999999999999999999966554 999999999999999999998744 3 79999999988755
No 11
>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=54.08 E-value=89 Score=24.96 Aligned_cols=55 Identities=11% Similarity=0.096 Sum_probs=37.9
Q ss_pred HHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHH---hhCCeEEEEEccEEEEeccCC
Q 014482 202 LNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLED---KTFGKIIFRHGGTLVLYRGRN 257 (423)
Q Consensus 202 V~eI~~aLk~hELVKIK~l~~~~~dmkeiae~Lee---kTggeVVq~IG~viVLYRg~n 257 (423)
+.+|-++++....|=+.+.....++.+++.+.|.. ..+|.+.+. |..++|+=+++
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 45688999999999999999999999999888875 678888776 55566665544
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=53.41 E-value=65 Score=25.75 Aligned_cols=53 Identities=11% Similarity=0.164 Sum_probs=37.7
Q ss_pred hhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHh---hcCCEEEEEeCCEEE
Q 014482 316 YGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRD---LVPCILVTFEKEQIV 369 (423)
Q Consensus 316 ~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLae---lTg~~lVq~iG~~IV 369 (423)
|+++. .|-++++...+|=+++......+.+++.++|+. ..+|.+..+-.+.++
T Consensus 9 ~~D~~-~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i~~~~~l 64 (73)
T PF04472_consen 9 FEDAR-EIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKISEKVFL 64 (73)
T ss_dssp GGGHH-HHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEEETTEEE
T ss_pred HHHHH-HHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEEcCCEEE
Confidence 34444 477799999999999999999999999999987 679998888555444
No 13
>PRK12465 xylose isomerase; Provisional
Probab=36.39 E-value=18 Score=39.02 Aligned_cols=19 Identities=32% Similarity=0.594 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCCCCCcccc
Q 014482 114 EPKYSPFGPGRLEREWTGV 132 (423)
Q Consensus 114 ep~~~pfgp~~~~r~wtg~ 132 (423)
-+---|||++|+.|||.+.
T Consensus 62 ~~G~DpFG~~T~~rpw~~~ 80 (445)
T PRK12465 62 GNGADPFGPGTRAYPWDVG 80 (445)
T ss_pred CCCCCCCCCccCCCCcccC
Confidence 3344699999999999754
No 14
>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=34.63 E-value=1.1e+02 Score=23.79 Aligned_cols=58 Identities=14% Similarity=-0.018 Sum_probs=48.7
Q ss_pred eEEeccCCchhhHHHHHHHHH-----hcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEe
Q 014482 307 LTKLAKNGYYGSLVPMVRDAF-----LVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFE 364 (423)
Q Consensus 307 ifqLGKnGv~~~Lv~~V~eAl-----EkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~i 364 (423)
.+.|+++.=....+..+..+| ...+-|.|.-.|.+-.-.=.+|+.|++..+..++|+.
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 478899999999999999999 9999999999999999999999999998865555543
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=34.13 E-value=30 Score=31.86 Aligned_cols=67 Identities=7% Similarity=0.024 Sum_probs=44.9
Q ss_pred CCCCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHH------HHhcCceEEEEe-cCCCcccHHHHHHHHHh
Q 014482 286 IEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRD------AFLVSELVRIDC-QGLERSDYKKIGCKLRD 354 (423)
Q Consensus 286 ~e~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~e------AlEkrELVKI~v-l~n~~~D~keia~eLae 354 (423)
..+|+.+|.+.||+.-+.- .|.+|||.+..--+....+ .-+-.+.+|-.+ +=-+..|+.+++..|.+
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 4699999999999998875 8889999876554443211 111222444444 33345788888888887
No 16
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=34.06 E-value=27 Score=27.96 Aligned_cols=21 Identities=10% Similarity=0.006 Sum_probs=17.0
Q ss_pred ccCCCCCHHHHHHHHHcCCCC
Q 014482 284 TTIEGLSIEETKEMRKRGLAV 304 (423)
Q Consensus 284 ~~~e~LT~KQr~yLR~lA~~l 304 (423)
.-.+.+|+.|+.||+.++..-
T Consensus 11 tGDePmT~aQ~syL~tL~e~A 31 (57)
T PF11272_consen 11 TGDEPMTGAQASYLKTLSEEA 31 (57)
T ss_pred CCCCCCcHHHHHHHHHHHHHh
Confidence 345799999999999988653
No 17
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=31.46 E-value=1.1e+02 Score=24.89 Aligned_cols=39 Identities=15% Similarity=0.197 Sum_probs=24.3
Q ss_pred CCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEccEEEE
Q 014482 212 AEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVL 252 (423)
Q Consensus 212 hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG~viVL 252 (423)
+||+=||+.. .. +...-..+|++..+|.+|....+++++
T Consensus 2 rEl~LiKV~~-~~-~~r~ei~~l~~~f~a~ivd~~~~~~ii 40 (75)
T PF10369_consen 2 RELALIKVKA-TP-ENRSEILQLAEIFRARIVDVSPDSIII 40 (75)
T ss_dssp EEEEEEEEE--SC-HHHHHHHHHHHHTT-EEEEEETTEEEE
T ss_pred eEEEEEEEEC-Cc-cCHHHHHHHHHHhCCEEEEECCCEEEE
Confidence 3544444443 22 344445678888999999998888765
No 18
>PRK05474 xylose isomerase; Provisional
Probab=30.55 E-value=24 Score=38.06 Aligned_cols=16 Identities=38% Similarity=0.908 Sum_probs=13.6
Q ss_pred CCCCCCCCCCCCcccc
Q 014482 117 YSPFGPGRLEREWTGV 132 (423)
Q Consensus 117 ~~pfgp~~~~r~wtg~ 132 (423)
--|||++|+.|||...
T Consensus 55 ~DpFG~~T~~rpw~~~ 70 (437)
T PRK05474 55 ADPFGGGTFQRPWDQP 70 (437)
T ss_pred CCCCCCccccCCCcCC
Confidence 3589999999999854
No 19
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=29.22 E-value=1.7e+02 Score=27.44 Aligned_cols=57 Identities=12% Similarity=0.145 Sum_probs=39.3
Q ss_pred HHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCC--CcccHHHHHHHHHh
Q 014482 297 MRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGL--ERSDYKKIGCKLRD 354 (423)
Q Consensus 297 LR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n--~~~D~keia~eLae 354 (423)
+.+++.+-+|++-++-+|.|+.|++.++.+.+.. .+.=..... --+|++++.+.|.+
T Consensus 119 ~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~~g-fi~~~~~~~~~~~d~~~e~~~~i~~ 177 (178)
T TIGR00730 119 WAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQEG-FISESHLKLIHVVSRPDELIEQVQN 177 (178)
T ss_pred HHHcCCCCCCEEEECCcchHHHHHHHHHHHHHCC-CCCHHHcCcEEEcCCHHHHHHHHHh
Confidence 5677888899999999999999999888655543 211111111 14678888887754
No 20
>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=28.86 E-value=27 Score=37.61 Aligned_cols=15 Identities=47% Similarity=1.108 Sum_probs=12.8
Q ss_pred CCCCCCCCCCCCccc
Q 014482 117 YSPFGPGRLEREWTG 131 (423)
Q Consensus 117 ~~pfgp~~~~r~wtg 131 (423)
--|||++|+.|||.+
T Consensus 54 ~DpFG~~T~~rpw~~ 68 (434)
T TIGR02630 54 GDPFGDGTADRPWDG 68 (434)
T ss_pred CCCCCCccCCCCCcc
Confidence 459999999999954
No 21
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=26.85 E-value=1.2e+02 Score=31.09 Aligned_cols=78 Identities=15% Similarity=0.106 Sum_probs=49.8
Q ss_pred HHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHh--hCCeEEEEEccE
Q 014482 172 AERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDK--TFGKIIFRHGGT 249 (423)
Q Consensus 172 kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~Leek--TggeVVq~IG~v 249 (423)
+....|+.... ..+-++-++-+||+-+-+.+|+..|+.+ .++++-.| +.=+..+....++. .....=+..|++
T Consensus 12 ~~v~~l~e~l~--~y~~v~vv~~~nv~s~ql~~iR~~LR~~--a~~~vgKN-TL~r~AL~~~~~~~~~l~~L~~~LkG~~ 86 (310)
T PTZ00135 12 AYFEKLYELLE--KYKKILIVSVDNVGSKQMQDIRRSLRGK--AELLMGKN-TLIRKALKQRLEELPELEKLLPHVKGNV 86 (310)
T ss_pred HHHHHHHHHHH--hCCEEEEEEcCCCCHHHHHHHHHHHhcC--CEEEEEeh-HHHHHHHhhCcccccChHHHHhhccCCE
Confidence 34567788775 7788999999999999999999999975 34555443 32222222222221 111122467888
Q ss_pred EEEec
Q 014482 250 LVLYR 254 (423)
Q Consensus 250 iVLYR 254 (423)
.++|=
T Consensus 87 gliFT 91 (310)
T PTZ00135 87 GFVFT 91 (310)
T ss_pred EEEEE
Confidence 88885
No 22
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=26.29 E-value=53 Score=30.18 Aligned_cols=28 Identities=29% Similarity=0.629 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHHhCCeeEEEeCCCCh
Q 014482 197 LTHNMLNDIHNHWKHAEAVRIKCLGVPT 224 (423)
Q Consensus 197 LT~~VV~eI~~aLk~hELVKIK~l~~~~ 224 (423)
|+++.|.+||++|.--+=|+|||++.+.
T Consensus 38 Ia~~fVkdI~d~L~vG~eV~vKVl~ide 65 (129)
T COG1098 38 IADGFVKDIHDHLKVGQEVKVKVLDIDE 65 (129)
T ss_pred hhhhhHHhHHHHhcCCCEEEEEEEeecc
Confidence 6899999999999999999999998643
No 23
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=26.07 E-value=1.2e+02 Score=31.15 Aligned_cols=63 Identities=16% Similarity=0.164 Sum_probs=46.2
Q ss_pred CHHHHHHHHHHHHhC--CeeEEEeCCCChH-hHHHHHHHHHHhhCCeEEEEE-------------ccEEEEeccCCCCC
Q 014482 198 THNMLNDIHNHWKHA--EAVRIKCLGVPTV-DMKNVCFQLEDKTFGKIIFRH-------------GGTLVLYRGRNYNP 260 (423)
Q Consensus 198 T~~VV~eI~~aLk~h--ELVKIK~l~~~~~-dmkeiae~LeekTggeVVq~I-------------G~viVLYRg~nY~p 260 (423)
-++|+++|.+-|..| |+|-+.+...... +-.+....|.+..|..++... .++||+|+...|..
T Consensus 93 ~~dvL~~i~~FL~~hp~EvVIL~~k~ey~~~~~~~~~~~li~~lGd~l~~~~~~~~~~TL~eL~~krVIviy~~~~~~~ 171 (285)
T cd08619 93 VDVVLNDIKRFLSETKSEFVILEIRTEYGHEDPPQFDLWLVEQLGDHLIHQDDSVFSKTLAELLPKRVICIWKPRKSPA 171 (285)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEEEeecccCCCchHHHHHHHHHhcchhccCCCccccccHHHHhCCcEEEEEcCCCCCc
Confidence 478999999999887 9999999754322 222556777788888887652 24688999887763
No 24
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=25.36 E-value=6.3e+02 Score=24.51 Aligned_cols=113 Identities=15% Similarity=0.080 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHh--CCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEccEEEEeccCCCCCCCCCcccccccCCCCC
Q 014482 199 HNMLNDIHNHWKH--AEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEP 276 (423)
Q Consensus 199 ~~VV~eI~~aLk~--hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG~viVLYRg~nY~p~~RpkIpLm~Wk~~~P 276 (423)
+.++++|...++. .-.+-+.+.+...++..++++.+++. |+..|...-+ .|...
T Consensus 83 ~~~~~~i~~~~~~~~~~pvi~si~g~~~~~~~~~a~~~~~~-G~d~ielN~~-----------------------cP~~~ 138 (289)
T cd02810 83 DVWLQDIAKAKKEFPGQPLIASVGGSSKEDYVELARKIERA-GAKALELNLS-----------------------CPNVG 138 (289)
T ss_pred HHHHHHHHHHHhccCCCeEEEEeccCCHHHHHHHHHHHHHh-CCCEEEEEcC-----------------------CCCCC
Confidence 4677788777764 34566777788888999999988876 7777776442 00000
Q ss_pred CCcCcccccCCCCCHHHHHHHHHcCCCCCceEEeccC-CchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhh
Q 014482 277 VYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKN-GYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDL 355 (423)
Q Consensus 277 v~p~ll~~~~e~LT~KQr~yLR~lA~~l~PifqLGKn-Gv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLael 355 (423)
.... ++++ .....+++.|+++...-=+||+.. ....++..+++..+.+
T Consensus 139 ~~~~-----------------------------~~~~~~~~~eiv~~vr~~~~~pv~vKl~~-~~~~~~~~~~a~~l~~- 187 (289)
T cd02810 139 GGRQ-----------------------------LGQDPEAVANLLKAVKAAVDIPLLVKLSP-YFDLEDIVELAKAAER- 187 (289)
T ss_pred CCcc-----------------------------cccCHHHHHHHHHHHHHccCCCEEEEeCC-CCCHHHHHHHHHHHHH-
Confidence 0000 1111 233456677776664444666663 2334467788887765
Q ss_pred cCCEEEEEeCC
Q 014482 356 VPCILVTFEKE 366 (423)
Q Consensus 356 Tg~~lVq~iG~ 366 (423)
.|++.|.+.+.
T Consensus 188 ~Gad~i~~~~~ 198 (289)
T cd02810 188 AGADGLTAINT 198 (289)
T ss_pred cCCCEEEEEcc
Confidence 68888888765
No 25
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=25.14 E-value=65 Score=27.95 Aligned_cols=26 Identities=42% Similarity=0.537 Sum_probs=16.3
Q ss_pred HHHHHHHHHHhhCCeEEEEEccEEEE
Q 014482 227 MKNVCFQLEDKTFGKIIFRHGGTLVL 252 (423)
Q Consensus 227 mkeiae~LeekTggeVVq~IG~viVL 252 (423)
.+.=-.+|.+.+||.|+.+.|++++|
T Consensus 19 I~~RL~qLsdNCGGkVl~v~~~tAil 44 (90)
T PF11608_consen 19 IKNRLRQLSDNCGGKVLSVSGGTAIL 44 (90)
T ss_dssp HHHHHHHHHHTTT--EEE--TT-EEE
T ss_pred HHHHHHHHhhccCCEEEEEeCCEEEE
Confidence 34445678899999999999998766
No 26
>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=24.03 E-value=5e+02 Score=23.26 Aligned_cols=82 Identities=16% Similarity=0.265 Sum_probs=38.9
Q ss_pred eEEEEEccEEEEeccCCCCCCCCCcccccccCCCCCCCcCcccccCCCCCHHHHHHHHHcCCCCCceEEeccCCchhhHH
Q 014482 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLV 320 (423)
Q Consensus 241 eVVq~IG~viVLYRg~nY~p~~RpkIpLm~Wk~~~Pv~p~ll~~~~e~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv 320 (423)
.|++..||.+=|.-+..|.... -.|....|+.+.-+.-.+..-+.++...|+++++..+-++.-+-.+--.++|
T Consensus 42 ~vt~~~GHl~~l~~p~~y~~~~------~~~~~~~p~~~~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I 115 (151)
T cd03362 42 VVTWASGHLLELDFPEEYDPWD------KVWPLEDPLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELI 115 (151)
T ss_pred EEEEEhhHhhcccChHHhccCC------CCCccccCCcCCceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHH
Confidence 5777788877665554443210 0121111222211111222335667777777777666665554333333444
Q ss_pred -HHHHHHHh
Q 014482 321 -PMVRDAFL 328 (423)
Q Consensus 321 -~~V~eAlE 328 (423)
..|.+++.
T Consensus 116 ~~~i~~~~~ 124 (151)
T cd03362 116 GREILEYAK 124 (151)
T ss_pred HHHHHHHhC
Confidence 34555554
No 27
>PRK10550 tRNA-dihydrouridine synthase C; Provisional
Probab=23.61 E-value=4.7e+02 Score=26.61 Aligned_cols=40 Identities=10% Similarity=0.008 Sum_probs=26.3
Q ss_pred hHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEE
Q 014482 318 SLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTF 363 (423)
Q Consensus 318 ~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~ 363 (423)
+.+..|+++ ++|-|-+|.....-+-|.++-+.+||+.|.+
T Consensus 184 ~~i~~ik~~------~~iPVi~nGdI~t~~da~~~l~~~g~DgVmi 223 (312)
T PRK10550 184 QAIGEIRQR------LTIPVIANGEIWDWQSAQQCMAITGCDAVMI 223 (312)
T ss_pred HHHHHHHhh------cCCcEEEeCCcCCHHHHHHHHhccCCCEEEE
Confidence 445666644 3567777777655556666657799988875
No 28
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=23.37 E-value=2.1e+02 Score=25.67 Aligned_cols=49 Identities=14% Similarity=0.158 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEE
Q 014482 194 RDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIF 244 (423)
Q Consensus 194 K~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq 244 (423)
..-+|+++++.|..++....=+.|.+.|. +|+-.+-..|..-.|+.|++
T Consensus 43 pG~It~el~~ai~~a~~~~~~~~I~V~GE--EDL~~lPail~aP~gs~V~Y 91 (121)
T PF04019_consen 43 PGTITEELIEAIKKALESGKPVVIFVDGE--EDLAVLPAILYAPEGSVVLY 91 (121)
T ss_pred CCcccHHHHHHHHHHHhCCCCEEEEEeCh--HHHHHHHHHHhCCCCCEEEE
Confidence 47799999999999999999999999885 78888888898888888887
No 29
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e 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. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 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, L10 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 WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=22.61 E-value=60 Score=30.22 Aligned_cols=68 Identities=10% Similarity=0.074 Sum_probs=45.5
Q ss_pred CCCCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHH---Hh-cCceEEEEe-cCCCcccHHHHHHHHHh
Q 014482 286 IEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDA---FL-VSELVRIDC-QGLERSDYKKIGCKLRD 354 (423)
Q Consensus 286 ~e~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eA---lE-krELVKI~v-l~n~~~D~keia~eLae 354 (423)
..+|+..|.+.||+.-+.- ..|.+|||.+..--+....+. |+ -.++++-.+ +=-++.|+.+++..|++
T Consensus 25 ~~gl~~~ql~~lR~~lr~~-~~~~v~KNtL~~~Al~~~~~~~~~~~~L~~~l~G~~~liFt~~dp~~v~k~l~~ 97 (175)
T cd05795 25 ADNVGSKQLQKIRRSLRGK-AEILMGKNTLIRRALRNLGDENPELEKLLPYLKGNVGFIFTNGDPFEIRKILEE 97 (175)
T ss_pred ecCCChHHHHHHHHHhhCC-CEEEEechHHHHHHHHhcccccccHHHHHHHhcCCEEEEEECCCHHHHHHHHHH
Confidence 4699999999999998863 788999998876555443210 11 123344433 33345788888888876
No 30
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=22.42 E-value=1.1e+02 Score=27.05 Aligned_cols=35 Identities=11% Similarity=0.227 Sum_probs=29.4
Q ss_pred HHHHcCCCCC-ceEEeccCCchhhHHHHHHHHHhcC
Q 014482 296 EMRKRGLAVP-VLTKLAKNGYYGSLVPMVRDAFLVS 330 (423)
Q Consensus 296 yLR~lA~~l~-PifqLGKnGv~~~Lv~~V~eAlEkr 330 (423)
-|.+++.+-+ |++-++.+|.++.++++++.+.+..
T Consensus 75 ~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g 110 (133)
T PF03641_consen 75 TLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEG 110 (133)
T ss_dssp HHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTT
T ss_pred HHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCC
Confidence 3577888888 9999999999999999998666544
No 31
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=21.96 E-value=2.2e+02 Score=30.70 Aligned_cols=88 Identities=19% Similarity=0.320 Sum_probs=59.5
Q ss_pred hhCCeEEE-EEccEEEEeccCCCCC-CCCCcccccccCCCCCCCcCccccc-------CCCCCHHHHHHHHHc-------
Q 014482 237 KTFGKIIF-RHGGTLVLYRGRNYNP-KKRPVIPLMLWRPHEPVYPKLIKTT-------IEGLSIEETKEMRKR------- 300 (423)
Q Consensus 237 kTggeVVq-~IG~viVLYRg~nY~p-~~RpkIpLm~Wk~~~Pv~p~ll~~~-------~e~LT~KQr~yLR~l------- 300 (423)
-+||..++ +.|...|+|-| +|+- +.|.-- --|- .++-|+||-.. -+.=.-+||.+|++-
T Consensus 158 VLGAaMf~ikvGd~svvYTG-DYnmTpDrHLG--aA~i--d~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~G 232 (501)
T KOG1136|consen 158 VLGAAMFYIKVGDQSVVYTG-DYNMTPDRHLG--AAWI--DKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARG 232 (501)
T ss_pred ccceeEEEEEecceeEEEec-CccCCcccccc--hhhh--ccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcC
Confidence 46788887 68999999998 6772 222110 1222 34667766432 235567899999974
Q ss_pred CCCCCceEEeccCCchhhHHHHHHHHHhcCce
Q 014482 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSEL 332 (423)
Q Consensus 301 A~~l~PifqLGKnGv~~~Lv~~V~eAlEkrEL 332 (423)
|.-|-|+|.||+. ++|.--+++.||.--|
T Consensus 233 GkvlIPvFALGRA---QElCiLLd~YWERm~l 261 (501)
T KOG1136|consen 233 GKVLIPVFALGRA---QELCILLDDYWERMNL 261 (501)
T ss_pred CeEEEEeeecchH---HHHHHHHHHHHHhhcc
Confidence 5678899999986 6777778889986543
No 32
>cd04734 OYE_like_3_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase.
Probab=20.84 E-value=5.7e+02 Score=26.19 Aligned_cols=48 Identities=13% Similarity=0.052 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHhCCeeEEEeCCCC-------hHhHHHHHHHHHHhhC-CeEEEEEcc
Q 014482 200 NMLNDIHNHWKHAEAVRIKCLGVP-------TVDMKNVCFQLEDKTF-GKIIFRHGG 248 (423)
Q Consensus 200 ~VV~eI~~aLk~hELVKIK~l~~~-------~~dmkeiae~LeekTg-geVVq~IG~ 248 (423)
.+|+.|++++-.+=.|+||+.... .+|..+++..|++ .| ...|.+.++
T Consensus 196 eiv~~ir~~vg~~~~v~iRl~~~~~~~~G~~~~e~~~~~~~l~~-~G~vd~i~vs~g 251 (343)
T cd04734 196 EVLAAVRAAVGPDFIVGIRISGDEDTEGGLSPDEALEIAARLAA-EGLIDYVNVSAG 251 (343)
T ss_pred HHHHHHHHHcCCCCeEEEEeehhhccCCCCCHHHHHHHHHHHHh-cCCCCEEEeCCC
Confidence 677788877765667999987532 4566677777776 44 577887655
No 33
>cd02933 OYE_like_FMN Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include 12-oxophytodienoate reductase, pentaerythritol tetranitrate reductase, morphinone reductase, and related enzymes.
Probab=20.79 E-value=7.2e+02 Score=25.48 Aligned_cols=47 Identities=9% Similarity=0.072 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhCCeeEEEeCCC----------ChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482 199 HNMLNDIHNHWKHAEAVRIKCLGV----------PTVDMKNVCFQLEDKTFGKIIFRHG 247 (423)
Q Consensus 199 ~~VV~eI~~aLk~hELVKIK~l~~----------~~~dmkeiae~LeekTggeVVq~IG 247 (423)
-.+|+.|.+++-.+ .|-||+... ..+++.+++..|++. |...|.+.+
T Consensus 206 ~eii~air~~vg~d-~v~vRis~~~~~~~~~~~~~~ee~~~~~~~l~~~-g~d~i~vs~ 262 (338)
T cd02933 206 LEVVDAVAEAIGAD-RVGIRLSPFGTFNDMGDSDPEATFSYLAKELNKR-GLAYLHLVE 262 (338)
T ss_pred HHHHHHHHHHhCCC-ceEEEECccccCCCCCCCCCHHHHHHHHHHHHHc-CCcEEEEec
Confidence 36788888887544 588888532 346667788888654 667777643
No 34
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=20.36 E-value=2.5e+02 Score=23.12 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHh
Q 014482 317 GSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRD 354 (423)
Q Consensus 317 ~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLae 354 (423)
..+++.+.+|+++.. +.++||+.|++
T Consensus 19 ~~~~~~~~~a~~~~~------------~~~eiA~~iK~ 44 (89)
T PF01221_consen 19 EEAIELAKEALKKYQ------------DEKEIAEFIKQ 44 (89)
T ss_dssp HHHHHHHHHHHHHCS------------SHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCC------------cHHHHHHHHHH
Confidence 345677777777444 55889999997
No 35
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e 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. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 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, L10 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 WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=20.22 E-value=1.6e+02 Score=27.46 Aligned_cols=47 Identities=13% Similarity=0.072 Sum_probs=37.1
Q ss_pred HHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCC
Q 014482 172 AERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGV 222 (423)
Q Consensus 172 kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~ 222 (423)
+....|+.... .-+-++-+.-+|++-+-+.+|+..|+.. +++++-.|
T Consensus 5 ~~v~el~e~l~--~~~~v~v~~~~gl~~~ql~~lR~~lr~~--~~~~v~KN 51 (175)
T cd05795 5 EYVEKLTELLK--SYPKVLIVDADNVGSKQLQKIRRSLRGK--AEILMGKN 51 (175)
T ss_pred HHHHHHHHHHH--hCCEEEEEEecCCChHHHHHHHHHhhCC--CEEEEech
Confidence 45667777775 6778888999999999999999999975 66666444
No 36
>cd02931 ER_like_FMN Enoate reductase (ER)-like FMN-binding domain. Enoate reductase catalyzes the NADH-dependent reduction of carbon-carbon double bonds of several molecules, including nonactivated 2-enoates, alpha,beta-unsaturated aldehydes, cyclic ketones, and methylketones. ERs are similar to 2,4-dienoyl-CoA reductase from E. coli and to the old yellow enzyme from Saccharomyces cerevisiae.
Probab=20.14 E-value=5.7e+02 Score=26.63 Aligned_cols=49 Identities=10% Similarity=0.030 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhCCeeEEEeCC---------------------CChHhHHHHHHHHHHhhCCeEEEEEccE
Q 014482 200 NMLNDIHNHWKHAEAVRIKCLG---------------------VPTVDMKNVCFQLEDKTFGKIIFRHGGT 249 (423)
Q Consensus 200 ~VV~eI~~aLk~hELVKIK~l~---------------------~~~~dmkeiae~LeekTggeVVq~IG~v 249 (423)
.+|+.|++++-.+=.|=||+.. ...++..+++..|++. |...|.+.++.
T Consensus 206 eii~~vr~~~g~~f~v~vri~~~~~~~~~~~~~~~~~~~~~~g~~~e~~~~~~~~l~~~-gvD~l~vs~g~ 275 (382)
T cd02931 206 EIVEEIKARCGEDFPVSLRYSVKSYIKDLRQGALPGEEFQEKGRDLEEGLKAAKILEEA-GYDALDVDAGS 275 (382)
T ss_pred HHHHHHHHhcCCCceEEEEEechhhccccccccccccccccCCCCHHHHHHHHHHHHHh-CCCEEEeCCCC
Confidence 6677777776444356666542 2335667788888654 78899988873
Done!