Query 042428
Match_columns 106
No_of_seqs 98 out of 100
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 06:05:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042428.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042428hhsearch_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 99.8 1.2E-21 2.5E-26 131.7 4.7 69 1-70 12-84 (84)
2 TIGR00253 RNA_bind_YhbY putati 99.8 4.7E-19 1E-23 123.1 7.1 73 1-73 12-88 (95)
3 PRK10343 RNA-binding protein Y 99.7 2.7E-17 5.9E-22 114.8 7.8 73 1-73 14-90 (97)
4 KOG1990 Poly(A)-specific exori 99.7 8.6E-18 1.9E-22 144.5 1.0 87 1-87 394-488 (564)
5 COG1534 Predicted RNA-binding 99.6 7.3E-16 1.6E-20 108.1 6.7 74 1-74 13-90 (97)
6 KOG1990 Poly(A)-specific exori 97.3 0.00021 4.5E-09 62.3 3.0 73 12-84 34-110 (564)
7 PF12813 XPG_I_2: XPG domain c 64.2 14 0.00031 29.0 4.6 47 17-68 6-55 (246)
8 PF02288 Dehydratase_MU: Dehyd 59.4 29 0.00063 24.7 5.0 62 16-82 18-86 (112)
9 PF04530 Viral_Beta_CD: Viral 54.4 10 0.00022 27.9 2.0 21 9-30 93-113 (122)
10 COG1098 VacB Predicted RNA bin 51.5 13 0.00029 27.6 2.2 26 16-41 38-63 (129)
11 KOG2925 Predicted translation 43.4 15 0.00032 28.3 1.5 22 76-97 119-140 (167)
12 smart00492 HELICc3 helicase su 36.2 88 0.0019 22.4 4.5 56 20-77 3-67 (141)
13 PHA00692 hypothetical protein 35.3 16 0.00035 24.3 0.5 20 14-33 55-74 (74)
14 COG0324 MiaA tRNA delta(2)-iso 34.1 36 0.00078 28.2 2.5 40 40-79 10-52 (308)
15 KOG1257 NADP+-dependent malic 33.3 44 0.00096 30.3 3.0 55 4-61 387-445 (582)
16 COG1697 DNA topoisomerase VI, 31.3 1.1E+02 0.0023 26.3 4.9 55 5-61 183-237 (356)
17 KOG0465 Mitochondrial elongati 31.0 67 0.0014 29.8 3.8 44 8-52 192-238 (721)
18 PF08740 BCS1_N: BCS1 N termin 30.8 1.4E+02 0.0031 21.5 5.0 44 31-75 127-170 (187)
19 PRK06934 flavodoxin; Provision 29.4 48 0.001 26.0 2.4 34 38-71 65-99 (221)
20 PF12636 DUF3781: Protein of u 28.9 6.8 0.00015 26.4 -2.1 45 27-74 7-51 (73)
21 PF10996 Beta-Casp: Beta-Casp 28.7 1.1E+02 0.0025 20.3 3.9 36 18-53 2-40 (126)
22 TIGR00285 DNA-binding protein 28.2 2E+02 0.0044 19.8 5.1 55 7-61 2-56 (87)
23 KOG3728 Uridine phosphorylase 26.2 1E+02 0.0022 25.7 3.8 38 34-71 52-90 (308)
24 PRK04015 DNA/RNA-binding prote 25.7 2.3E+02 0.0051 19.6 5.1 57 5-61 3-59 (91)
25 cd08586 PI-PLCc_BcPLC_like Cat 24.8 2.5E+02 0.0054 22.4 5.8 57 15-71 73-149 (279)
26 TIGR00090 iojap_ybeB iojap-lik 24.1 95 0.0021 21.1 2.8 23 35-57 32-54 (99)
27 cd01789 Alp11_N Ubiquitin-like 23.2 2.2E+02 0.0048 18.5 5.0 52 42-105 21-72 (84)
28 PF14560 Ubiquitin_2: Ubiquiti 23.1 1.6E+02 0.0035 18.9 3.7 51 44-105 24-74 (87)
29 smart00148 PLCXc Phospholipase 21.4 2.1E+02 0.0045 20.3 4.2 46 16-61 70-118 (135)
30 PF01918 Alba: Alba; InterPro 21.1 2.1E+02 0.0046 17.5 4.8 50 9-58 3-57 (70)
31 COG0799 Uncharacterized homolo 21.1 1.1E+02 0.0024 22.1 2.8 22 36-57 38-59 (115)
32 COG0088 RplD Ribosomal protein 20.7 2E+02 0.0043 22.6 4.3 55 31-86 122-185 (214)
33 COG5616 Predicted integral mem 20.2 1.6E+02 0.0034 22.4 3.6 39 14-55 46-89 (152)
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=99.84 E-value=1.2e-21 Score=131.72 Aligned_cols=69 Identities=25% Similarity=0.283 Sum_probs=57.8
Q ss_pred CCccCCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC----CccEEEEec
Q 042428 1 MAQKRSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP----GVDVWLPSD 70 (106)
Q Consensus 1 ~g~kmk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv----gg~~ii~yR 70 (106)
+|+.++|.++|||+|||++|+++|+.+|+.||||||+|.+++..+++++|++||++|||++ |..+++ ||
T Consensus 12 ~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~vl-yR 84 (84)
T PF01985_consen 12 LAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTIVL-YR 84 (84)
T ss_dssp HHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEEEE-EE
T ss_pred HhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEEEE-EC
Confidence 3688999999999999999999999999999999999999999999999999999999999 555555 54
No 2
>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=99.78 E-value=4.7e-19 Score=123.06 Aligned_cols=73 Identities=16% Similarity=0.180 Sum_probs=68.9
Q ss_pred CCccCCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC----CccEEEEecCCC
Q 042428 1 MAQKRSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP----GVDVWLPSDSLG 73 (106)
Q Consensus 1 ~g~kmk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv----gg~~ii~yRgkn 73 (106)
+|+.++|.++|||+|+|++|+++++++|++||||||++.+++..+.+++|++|++.||+.+ |..++||+++++
T Consensus 12 ~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~vlYR~~~~ 88 (95)
T TIGR00253 12 KAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTIVLYRPTKE 88 (95)
T ss_pred HhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEEEEEecCCc
Confidence 5789999999999999999999999999999999999999999999999999999999999 888888777654
No 3
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.71 E-value=2.7e-17 Score=114.84 Aligned_cols=73 Identities=18% Similarity=0.187 Sum_probs=69.3
Q ss_pred CCccCCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC----CccEEEEecCCC
Q 042428 1 MAQKRSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP----GVDVWLPSDSLG 73 (106)
Q Consensus 1 ~g~kmk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv----gg~~ii~yRgkn 73 (106)
+|+.++|.++||+.|+|++|++++..+++.|||+||++.+++..+.++++++|++.||+.+ |..++||+++++
T Consensus 14 ~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~vlYR~~~~ 90 (97)
T PRK10343 14 LAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKE 90 (97)
T ss_pred hcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEEEEEecCCC
Confidence 5889999999999999999999999999999999999999999999999999999999999 888999888753
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.67 E-value=8.6e-18 Score=144.50 Aligned_cols=87 Identities=34% Similarity=0.427 Sum_probs=79.7
Q ss_pred CCccCCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCCh-hhHHHHHHHHHHHcCCCC-------CccEEEEecCC
Q 042428 1 MAQKRSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKP-GQINEFAEEIARLSVPPP-------GVDVWLPSDSL 72 (106)
Q Consensus 1 ~g~kmk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~-~~~~e~ae~Le~~sGGiv-------gg~~ii~yRgk 72 (106)
+|++|++++.+|++|+|+|+++|||+|||++|++|++|++... .+++..|..+++++||++ .+.+++.|||+
T Consensus 394 ~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k 473 (564)
T KOG1990|consen 394 VGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGK 473 (564)
T ss_pred HHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhh
Confidence 5789999999999999999999999999999999999999988 999999999999999999 55669999999
Q ss_pred CCCCCccccccCCCC
Q 042428 73 GTAFPQVDIEDAGLS 87 (106)
Q Consensus 73 nY~~P~~~~~~~~~~ 87 (106)
||++|..+-+.+-++
T Consensus 474 ~y~~p~~l~P~~~l~ 488 (564)
T KOG1990|consen 474 NYDRPTSLRPRNLLS 488 (564)
T ss_pred hccCCcccCchhhhc
Confidence 999999965555544
No 5
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.63 E-value=7.3e-16 Score=108.09 Aligned_cols=74 Identities=20% Similarity=0.209 Sum_probs=68.7
Q ss_pred CCccCCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC----CccEEEEecCCCC
Q 042428 1 MAQKRSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP----GVDVWLPSDSLGT 74 (106)
Q Consensus 1 ~g~kmk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv----gg~~ii~yRgknY 74 (106)
+|..++|.++|||.|||++|+.+|..++++||||||++.+++..+-+++|+.|++++|+.+ |..++||++|+..
T Consensus 13 ~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~vlyr~~~e~ 90 (97)
T COG1534 13 KAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTLVLYRESKEK 90 (97)
T ss_pred hhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEEEEEecCccc
Confidence 4788999999999999999999999999999999999999999999999999999999999 7778887766643
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.25 E-value=0.00021 Score=62.30 Aligned_cols=73 Identities=11% Similarity=-0.052 Sum_probs=63.1
Q ss_pred CCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC----CccEEEEecCCCCCCCccccccC
Q 042428 12 GRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP----GVDVWLPSDSLGTAFPQVDIEDA 84 (106)
Q Consensus 12 GKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv----gg~~ii~yRgknY~~P~~~~~~~ 84 (106)
+++|++.++++.+++-||.+|+++++|..-...+|+.+++.++..+||-+ .|...-.|++..|..|..-.+..
T Consensus 34 ~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~ 110 (564)
T KOG1990|consen 34 WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ 110 (564)
T ss_pred cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeeeecCccccCCccceeecchhhhhhh
Confidence 99999999999999999999999999999999999999999999999955 33333334888888887766655
No 7
>PF12813 XPG_I_2: XPG domain containing
Probab=64.21 E-value=14 Score=29.02 Aligned_cols=47 Identities=19% Similarity=0.202 Sum_probs=37.1
Q ss_pred chhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC-Cc--cEEEE
Q 042428 17 FGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP-GV--DVWLP 68 (106)
Q Consensus 17 f~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv-gg--~~ii~ 68 (106)
.+.+++-+...|+....+.+ ++.+++..+..++++.||-| ++ +++|+
T Consensus 6 ~~~~~e~L~~~~~~~~~~~~-----~~~EAD~~~A~~A~~~~~~VLt~DSDf~I~ 55 (246)
T PF12813_consen 6 VPAFIEALRESWRYGVPVVQ-----CPGEADRECAALARKWGCPVLTNDSDFLIH 55 (246)
T ss_pred HHHHHHHHHHHhhcCCcEEE-----cCccchHHHHHHHHHcCCeEEccCCCEEEe
Confidence 46788999999997776665 47789999999999999988 33 45553
No 8
>PF02288 Dehydratase_MU: Dehydratase medium subunit; InterPro: IPR003208 This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.; PDB: 2D0P_B 2D0O_D 1IWP_E 1MMF_B 1NBW_B 3AUJ_B 1UC5_B 1IWB_B 1EEX_E 1DIO_B ....
Probab=59.39 E-value=29 Score=24.68 Aligned_cols=62 Identities=18% Similarity=0.108 Sum_probs=49.7
Q ss_pred cchhHHHHHHHhhhhcceeEEEe-cCCChhhHHHHHHHHHHHcCCCC------CccEEEEecCCCCCCCccccc
Q 042428 16 VFGGVILNMHMHWKKHEIVKVFC-KPSKPGQINEFAEEIARLSVPPP------GVDVWLPSDSLGTAFPQVDIE 82 (106)
Q Consensus 16 Vf~gVIeniH~hWK~rElVKI~~-~~~~~~~~~e~ae~Le~~sGGiv------gg~~ii~yRgknY~~P~~~~~ 82 (106)
++..|+..|. -|=|..++ ......++...|.+.++.|+=-| .|+++|-|+...-..|.+.+.
T Consensus 18 ~lrev~aGIE-----EEGip~~~~~~~~~~d~~~lA~~AA~~S~lgVGIGi~~~G~~vih~~~L~~~~pL~~~~ 86 (112)
T PF02288_consen 18 VLREVLAGIE-----EEGIPYRVVRVSDTSDVAFLAYQAARLSRLGVGIGIQSKGTIVIHYKDLPPLSPLFLFP 86 (112)
T ss_dssp HHHHHHHHHH-----CTT-EEEEEEECSSSSHHHHHHHHHHHSTTSEEEEE-TTSEEEEEETTS-TTS-SEEEE
T ss_pred HHHHHHhHhc-----ccCCCeEEEeecCcccHHHHHHHHhhccCcceeEEEcCCCcEEEEcCCCCCCCCceecc
Confidence 7777888888 67777777 66777899999999999999888 558999999999989999877
No 9
>PF04530 Viral_Beta_CD: Viral Beta C/D like family; InterPro: IPR007617 This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Probab=54.43 E-value=10 Score=27.95 Aligned_cols=21 Identities=29% Similarity=0.513 Sum_probs=18.6
Q ss_pred cccCCCccchhHHHHHHHhhhh
Q 042428 9 LPSGRRRVFGGVILNMHMHWKK 30 (106)
Q Consensus 9 L~IGKrGVf~gVIeniH~hWK~ 30 (106)
+.+|...|-+.||+.|| ||.+
T Consensus 93 ik~~~~PIDP~VIaAIH-HwQk 113 (122)
T PF04530_consen 93 IKLAPVPIDPEVIAAIH-HWQK 113 (122)
T ss_pred EecCCCCCCHHHHHHHH-HHHh
Confidence 56799999999999999 9975
No 10
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=51.53 E-value=13 Score=27.57 Aligned_cols=26 Identities=27% Similarity=0.294 Sum_probs=23.5
Q ss_pred cchhHHHHHHHhhhhcceeEEEecCC
Q 042428 16 VFGGVILNMHMHWKKHEIVKVFCKPS 41 (106)
Q Consensus 16 Vf~gVIeniH~hWK~rElVKI~~~~~ 41 (106)
|.+|.|.+||+|++--+-|+|+++..
T Consensus 38 Ia~~fVkdI~d~L~vG~eV~vKVl~i 63 (129)
T COG1098 38 IADGFVKDIHDHLKVGQEVKVKVLDI 63 (129)
T ss_pred hhhhhHHhHHHHhcCCCEEEEEEEee
Confidence 57899999999999999999999864
No 11
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=43.38 E-value=15 Score=28.31 Aligned_cols=22 Identities=50% Similarity=0.583 Sum_probs=20.0
Q ss_pred CCccccccCCCCCCCCCCCCCc
Q 042428 76 FPQVDIEDAGLSTSESDHEDDS 97 (106)
Q Consensus 76 ~P~~~~~~~~~~~~~~~~~~~~ 97 (106)
.|..+++|.++|-|+++.+|||
T Consensus 119 ~t~e~~~dd~ls~sese~ddds 140 (167)
T KOG2925|consen 119 STIEQHEDDGLSDSESEDDDDS 140 (167)
T ss_pred CCcccccccCCCCcccccccCC
Confidence 4788999999999999999987
No 12
>smart00492 HELICc3 helicase superfamily c-terminal domain.
Probab=36.20 E-value=88 Score=22.38 Aligned_cols=56 Identities=9% Similarity=0.089 Sum_probs=37.2
Q ss_pred HHHHHHHhhhhcce-------eEEEecCCChhhHHHHHHHHHHHcC-CCC-CccEEEEecCCCCCCC
Q 042428 20 VILNMHMHWKKHEI-------VKVFCKPSKPGQINEFAEEIARLSV-PPP-GVDVWLPSDSLGTAFP 77 (106)
Q Consensus 20 VIeniH~hWK~rEl-------VKI~~~~~~~~~~~e~ae~Le~~sG-Giv-gg~~ii~yRgknY~~P 77 (106)
.++.++.+|+..-. -.|.+.+....+..++.+...+..+ +++ |... +.+|-++...
T Consensus 3 ~m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~--~~EGiD~~g~ 67 (141)
T smart00492 3 YMESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATAR--FSEGVDFPGD 67 (141)
T ss_pred HHHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccc--eecceecCCC
Confidence 46788999988665 4566656555566677777665543 666 4333 6888888765
No 13
>PHA00692 hypothetical protein
Probab=35.27 E-value=16 Score=24.32 Aligned_cols=20 Identities=25% Similarity=0.652 Sum_probs=14.6
Q ss_pred CccchhHHHHHHHhhhhcce
Q 042428 14 RRVFGGVILNMHMHWKKHEI 33 (106)
Q Consensus 14 rGVf~gVIeniH~hWK~rEl 33 (106)
+--.|-.+..|.+|||...|
T Consensus 55 araldvlltrmeqhwkdeql 74 (74)
T PHA00692 55 ARALDVLLTRMEQHWKDEQL 74 (74)
T ss_pred HHHHHHHHHHHHHhhccccC
Confidence 33456678899999998653
No 14
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=34.12 E-value=36 Score=28.19 Aligned_cols=40 Identities=20% Similarity=0.134 Sum_probs=30.6
Q ss_pred CCChhhHHHHHHHHHHHcCCCC-CccEEEEecCC--CCCCCcc
Q 042428 40 PSKPGQINEFAEEIARLSVPPP-GVDVWLPSDSL--GTAFPQV 79 (106)
Q Consensus 40 ~~~~~~~~e~ae~Le~~sGGiv-gg~~ii~yRgk--nY~~P~~ 79 (106)
+..+.---..|-.|+.++||+| +.+.+-+|||- +...|+.
T Consensus 10 GPTAsGKT~lai~LAk~~~~eIIs~DSmQvYr~mdIGTAKps~ 52 (308)
T COG0324 10 GPTASGKTALAIALAKRLGGEIISLDSMQVYRGLDIGTAKPSL 52 (308)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEecchhhhcCCCcccCCCCCH
Confidence 3333334478999999999999 99999999998 4556644
No 15
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=33.25 E-value=44 Score=30.26 Aligned_cols=55 Identities=15% Similarity=0.098 Sum_probs=49.5
Q ss_pred cCCCccccCCCcc----chhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC
Q 042428 4 KRSSCLPSGRRRV----FGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP 61 (106)
Q Consensus 4 kmk~~L~IGKrGV----f~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv 61 (106)
+.||-+.||-.|+ |+.|++.|+.+ +|-=-|..+-|+..++.-+||+.=+-|+|-.
T Consensus 387 ~vKPtvLiG~S~~~g~Fteevl~~Ma~~---~erPiIFalSNPT~~aECtae~ay~~t~Gr~ 445 (582)
T KOG1257|consen 387 EVKPTVLIGASGVGGAFTEEVLRAMAKS---NERPIIFALSNPTSKAECTAEQAYKWTKGRA 445 (582)
T ss_pred hcCCcEEEecccCCccCCHHHHHHHHhc---CCCceEEecCCCccccccCHHHHhhhcCCcE
Confidence 5789999998876 78999999976 7777889999999999999999999999987
No 16
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=31.34 E-value=1.1e+02 Score=26.29 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=47.8
Q ss_pred CCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC
Q 042428 5 RSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP 61 (106)
Q Consensus 5 mk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv 61 (106)
++-.|-|=+.|||+-.+++.+ |+....+-|..++.+...++.+-..|+.+++--|
T Consensus 183 a~~VlvVEk~avf~rLv~e~~--~~k~nailVt~KGqP~raTRrflkrL~eel~lpv 237 (356)
T COG1697 183 AKFVLVVEKDAVFQRLVEEGF--WEKENAILVTLKGQPDRATRRFLKRLNEELDLPV 237 (356)
T ss_pred ceEEEEEechHHHHHHHHhhh--hhhcCeEEEecCCCccHHHHHHHHHHHHHhCCCE
Confidence 445677789999999999875 9999999999999999999999999999986555
No 17
>KOG0465 consensus Mitochondrial elongation factor [Translation, ribosomal structure and biogenesis]
Probab=31.02 E-value=67 Score=29.84 Aligned_cols=44 Identities=27% Similarity=0.382 Sum_probs=34.5
Q ss_pred ccccCCCccchhHHHHHHHh---hhhcceeEEEecCCChhhHHHHHHH
Q 042428 8 CLPSGRRRVFGGVILNMHMH---WKKHEIVKVFCKPSKPGQINEFAEE 52 (106)
Q Consensus 8 ~L~IGKrGVf~gVIeniH~h---WK~rElVKI~~~~~~~~~~~e~ae~ 52 (106)
++++|..++|.||++.++.+ |.-..--.|+. +.-+.++++.|++
T Consensus 192 qiPig~e~~f~GvvDlv~~kai~~~g~~g~~i~~-~eIP~~l~~~~~e 238 (721)
T KOG0465|consen 192 QIPIGSESNFKGVVDLVNGKAIYWDGENGEIVRK-DEIPEDLEELAEE 238 (721)
T ss_pred EccccccccchhHHhhhhceEEEEcCCCCceeEe-ccCCHHHHHHHHH
Confidence 57899999999999999975 77776666666 6666777766654
No 18
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=30.77 E-value=1.4e+02 Score=21.46 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=31.8
Q ss_pred cceeEEEecCCChhhHHHHHHHHHHHcCCCCCccEEEEecCCCCC
Q 042428 31 HEIVKVFCKPSKPGQINEFAEEIARLSVPPPGVDVWLPSDSLGTA 75 (106)
Q Consensus 31 rElVKI~~~~~~~~~~~e~ae~Le~~sGGivgg~~ii~yRgknY~ 75 (106)
.|.+.|.|.+-++.-.+++-++..+..-..-.+.. ++||..++.
T Consensus 127 ~e~l~l~~lg~s~~~l~~ll~ear~~~~~~~~~~t-~Iy~~~~~~ 170 (187)
T PF08740_consen 127 DETLTLSCLGRSPKPLKDLLEEAREYYLKKQKGKT-TIYRADGSE 170 (187)
T ss_pred ceEEEEEEecCCHHHHHHHHHHHHHHHHHhcCCcE-EEEeCCCCC
Confidence 89999999999988888887776666554444444 446666553
No 19
>PRK06934 flavodoxin; Provisional
Probab=29.37 E-value=48 Score=26.04 Aligned_cols=34 Identities=12% Similarity=-0.015 Sum_probs=25.2
Q ss_pred ecCCChhhHHHHHHHHHHHcCCCC-CccEEEEecC
Q 042428 38 CKPSKPGQINEFAEEIARLSVPPP-GVDVWLPSDS 71 (106)
Q Consensus 38 ~~~~~~~~~~e~ae~Le~~sGGiv-gg~~ii~yRg 71 (106)
..+....+++.+|+.|++++||.+ .....=.|.+
T Consensus 65 ~~~~~~GnTk~vAe~Ia~~~gaDl~eI~~~~~Y~~ 99 (221)
T PRK06934 65 KNGEVLGSTQYVAQIIQEETGGDLFRIETVKPYPR 99 (221)
T ss_pred cCCCCCCHHHHHHHHHHHHHCCCEEEEEEccccCC
Confidence 345566899999999999999999 4444433443
No 20
>PF12636 DUF3781: Protein of unknown function (DUF3781); InterPro: IPR024229 This family of functionally uncharacterised proteins is found in bacteria and archaea. These proteins are typically between 82 and 98 amino acids in length and have two conserved sequence motifs: GKNWY and ITA.
Probab=28.88 E-value=6.8 Score=26.41 Aligned_cols=45 Identities=9% Similarity=-0.090 Sum_probs=30.9
Q ss_pred hhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCCCccEEEEecCCCC
Q 042428 27 HWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPPGVDVWLPSDSLGT 74 (106)
Q Consensus 27 hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGivgg~~ii~yRgknY 74 (106)
....-|+..++++.|...+...+.+-...+. ....+.|.++||||
T Consensus 7 klhtT~lG~~RIkrNL~l~~~dvVe~ck~~I---~~~~a~I~rkGKN~ 51 (73)
T PF12636_consen 7 KLHTTELGVVRIKRNLGLDTSDVVEWCKNKI---LDPNAKITRKGKNW 51 (73)
T ss_pred hhcCcHHHHHHHHhcCCCCcccHHHHHHHHH---cCchhhhhcCCceE
Confidence 4446777778888887776666655444332 25678889999998
No 21
>PF10996 Beta-Casp: Beta-Casp domain; InterPro: IPR022712 The beta-CASP domain is found C-terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains []. ; PDB: 2YCB_B 2XR1_B 2I7T_A 2I7V_A 2I7X_A 3A4Y_A 3IE2_D 3IE1_B 3IE0_D 2DKF_D ....
Probab=28.72 E-value=1.1e+02 Score=20.27 Aligned_cols=36 Identities=14% Similarity=0.415 Sum_probs=29.7
Q ss_pred hhHHHHHHHhhhhcce---eEEEecCCChhhHHHHHHHH
Q 042428 18 GGVILNMHMHWKKHEI---VKVFCKPSKPGQINEFAEEI 53 (106)
Q Consensus 18 ~gVIeniH~hWK~rEl---VKI~~~~~~~~~~~e~ae~L 53 (106)
..++.=++++|+...+ +.|.+....+..+-+++...
T Consensus 2 qEll~~L~~~~~~~~~~~~~pI~~~s~~a~~~~~~~~~~ 40 (126)
T PF10996_consen 2 QELLLILDEYWKEGKLPRDVPIYVDSPMAAKVLEYYKSY 40 (126)
T ss_dssp HHHHHHHHHHHCTTSSGTTSEEEEESTCHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHhCCCCCCCcEEEEChHHHHHHHHHHHH
Confidence 5688889999998874 99999998888888877553
No 22
>TIGR00285 DNA-binding protein Alba. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
Probab=28.23 E-value=2e+02 Score=19.83 Aligned_cols=55 Identities=13% Similarity=0.091 Sum_probs=46.2
Q ss_pred CccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC
Q 042428 7 SCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP 61 (106)
Q Consensus 7 ~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv 61 (106)
+.+.||+.+|..=|+.=+++-=+...-|.|+..+..-..+-.+||.+.++....+
T Consensus 2 ~~i~vG~KPvmnYVlavlt~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~v 56 (87)
T TIGR00285 2 NVVYIGNKPVMNYVLAVLTQLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPDI 56 (87)
T ss_pred CEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCCc
Confidence 4578999999998888888655556778899999999999999999999876554
No 23
>KOG3728 consensus Uridine phosphorylase [Nucleotide transport and metabolism]
Probab=26.25 E-value=1e+02 Score=25.73 Aligned_cols=38 Identities=24% Similarity=0.241 Sum_probs=29.4
Q ss_pred eEEEecCCChhhHHHHHHHHHHHcCCCC-CccEEEEecC
Q 042428 34 VKVFCKPSKPGQINEFAEEIARLSVPPP-GVDVWLPSDS 71 (106)
Q Consensus 34 VKI~~~~~~~~~~~e~ae~Le~~sGGiv-gg~~ii~yRg 71 (106)
||.+|.+-++..|+.+|.-+..+.|=.. ++..=|.-|+
T Consensus 52 vkfVC~GGtp~Rmk~~a~~~~~el~~~~~~~~~di~a~s 90 (308)
T KOG3728|consen 52 VKFVCMGGTPSRMKQFALYLRDELGVSCSGDPVDICARS 90 (308)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHhCCCCCCCCcchhccc
Confidence 8999999999999999999999977555 4433333333
No 24
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=25.68 E-value=2.3e+02 Score=19.61 Aligned_cols=57 Identities=12% Similarity=0.124 Sum_probs=47.9
Q ss_pred CCCccccCCCccchhHHHHHHHhhhhcceeEEEecCCChhhHHHHHHHHHHHcCCCC
Q 042428 5 RSSCLPSGRRRVFGGVILNMHMHWKKHEIVKVFCKPSKPGQINEFAEEIARLSVPPP 61 (106)
Q Consensus 5 mk~~L~IGKrGVf~gVIeniH~hWK~rElVKI~~~~~~~~~~~e~ae~Le~~sGGiv 61 (106)
..+.+.||+.+++.=|..-+++-=+...=|.|+..+..-..+-.+||.|.++...-+
T Consensus 3 ~en~i~Ig~kpvmnYV~~~~~~l~~g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v 59 (91)
T PRK04015 3 EENVVLVGKKPVMNYVLAVLTQFNQGAKEVVIKARGRAISKAVDVAEIVRNRFLPDV 59 (91)
T ss_pred CCCEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEeccccchhhhHHHHHHHhccCCe
Confidence 356789999999998888888744567788899999999999999999999876545
No 25
>cd08586 PI-PLCc_BcPLC_like Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins. This subfamily corresponds to the catalytic domain present in Bacillus cereus phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and its sequence homologs found in bacteria and eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Their catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This family also includes some uncharacterized eukaryotic homologs, which
Probab=24.83 E-value=2.5e+02 Score=22.38 Aligned_cols=57 Identities=19% Similarity=0.170 Sum_probs=41.5
Q ss_pred ccchhHHHHHHHhhhh--cceeEEEecCCChhh--HHHHHHHHHHHcCC-----------CC-----CccEEEEecC
Q 042428 15 RVFGGVILNMHMHWKK--HEIVKVFCKPSKPGQ--INEFAEEIARLSVP-----------PP-----GVDVWLPSDS 71 (106)
Q Consensus 15 GVf~gVIeniH~hWK~--rElVKI~~~~~~~~~--~~e~ae~Le~~sGG-----------iv-----gg~~ii~yRg 71 (106)
.-|+.|++++..=.+. .|+|-+.+++....+ ..++++.++..... .+ -|+++|+.|-
T Consensus 73 ~~~~dvL~~i~~FL~~nP~E~Vil~l~~e~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~PtLge~RGKIVLl~rf 149 (279)
T cd08586 73 LTFGDVLNECYSFLDANPSETIIMSLKQEGSGDGNTDSFAEIFKEYLDNYPSYFYYTESKIPTLGEVRGKIVLLRRF 149 (279)
T ss_pred CcHHHHHHHHHHHHHhCCCcEEEEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCCCchHHhcccEEEEEec
Confidence 5689999999987777 499999999877664 67777777644221 22 5678888773
No 26
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=24.06 E-value=95 Score=21.13 Aligned_cols=23 Identities=9% Similarity=0.173 Sum_probs=20.1
Q ss_pred EEEecCCChhhHHHHHHHHHHHc
Q 042428 35 KVFCKPSKPGQINEFAEEIARLS 57 (106)
Q Consensus 35 KI~~~~~~~~~~~e~ae~Le~~s 57 (106)
-|+|..++..+++.+|+.+....
T Consensus 32 ~VI~Tg~S~rh~~aia~~v~~~~ 54 (99)
T TIGR00090 32 FVIASGTSSRHVKAIADNVEEEL 54 (99)
T ss_pred EEEEEeCCHHHHHHHHHHHHHHH
Confidence 47899999999999999988764
No 27
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=23.17 E-value=2.2e+02 Score=18.46 Aligned_cols=52 Identities=15% Similarity=0.206 Sum_probs=35.4
Q ss_pred ChhhHHHHHHHHHHHcCCCCCccEEEEecCCCCCCCccccccCCCCCCCCCCCCCccceeecCC
Q 042428 42 KPGQINEFAEEIARLSVPPPGVDVWLPSDSLGTAFPQVDIEDAGLSTSESDHEDDSLSIFPLKN 105 (106)
Q Consensus 42 ~~~~~~e~ae~Le~~sGGivgg~~ii~yRgknY~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (106)
+...+.+..+.|++.+|-.++..-+.+|.+++= .+. +-|.++.+|+-|++++
T Consensus 21 ~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~-~~~-----------~l~~d~~~L~~y~~~d 72 (84)
T cd01789 21 RGLTIAELKKKLELVVGTPASSMRLQLFDGDDK-LVS-----------KLDDDDALLGSYPVDD 72 (84)
T ss_pred CCCcHHHHHHHHHHHHCCCccceEEEEEcCCCC-eEe-----------ecCCCccEeeeccCCC
Confidence 345678888999999988888888878888731 111 1345556677776654
No 28
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=23.13 E-value=1.6e+02 Score=18.92 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=31.8
Q ss_pred hhHHHHHHHHHHHcCCCCCccEEEEecCCCCCCCccccccCCCCCCCCCCCCCccceeecCC
Q 042428 44 GQINEFAEEIARLSVPPPGVDVWLPSDSLGTAFPQVDIEDAGLSTSESDHEDDSLSIFPLKN 105 (106)
Q Consensus 44 ~~~~e~ae~Le~~sGGivgg~~ii~yRgknY~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (106)
..+.+.-+.|+..+|-.++.--+.++...+-..+..+ +.++.+|+.|++++
T Consensus 24 ~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~-----------~dd~~~L~~y~~~d 74 (87)
T PF14560_consen 24 ITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEEL-----------DDDDATLGSYGIKD 74 (87)
T ss_dssp SBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEES-----------SGSSSBCCHHT-ST
T ss_pred CCHHHHHHHHHHHhCCCcccEEEEEEecCCCcccccc-----------CCCccEeecCCCCC
Confidence 4577889999999998887776666645544333222 44566677777654
No 29
>smart00148 PLCXc Phospholipase C, catalytic domain (part); domain X. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme [6] appears to be a homologue of the mammalian PLCs.
Probab=21.35 E-value=2.1e+02 Score=20.25 Aligned_cols=46 Identities=11% Similarity=-0.052 Sum_probs=35.8
Q ss_pred cchhHHHHHHHhhhh--cceeEEEecCC-ChhhHHHHHHHHHHHcCCCC
Q 042428 16 VFGGVILNMHMHWKK--HEIVKVFCKPS-KPGQINEFAEEIARLSVPPP 61 (106)
Q Consensus 16 Vf~gVIeniH~hWK~--rElVKI~~~~~-~~~~~~e~ae~Le~~sGGiv 61 (106)
-|+.|++.|.+-... .|.|-+.++.. +..+-+.+++.|..-.|..+
T Consensus 70 ~~~dvL~~i~~fl~~~p~e~VIl~l~~~~~~~~~~~l~~~l~~~~g~~l 118 (135)
T smart00148 70 KLSEVLEAIKDFAFVTSPYPVILSLENHCSPDQQAKMAQMFKEIFGDML 118 (135)
T ss_pred EHHHHHHHHHHHHHhCCCCcEEEeehhhCCHHHHHHHHHHHHHHHhHhh
Confidence 468899999988776 59999999855 45666788888888877655
No 30
>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=21.13 E-value=2.1e+02 Score=17.53 Aligned_cols=50 Identities=10% Similarity=-0.054 Sum_probs=41.4
Q ss_pred cccCCCccchhHHHHHHHhh-----hhcceeEEEecCCChhhHHHHHHHHHHHcC
Q 042428 9 LPSGRRRVFGGVILNMHMHW-----KKHEIVKVFCKPSKPGQINEFAEEIARLSV 58 (106)
Q Consensus 9 L~IGKrGVf~gVIeniH~hW-----K~rElVKI~~~~~~~~~~~e~ae~Le~~sG 58 (106)
+.|++..=+...++.+-.++ ...+-|.+...+.....+-.+||.+.++.+
T Consensus 3 I~V~~~~~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~ 57 (70)
T PF01918_consen 3 IYVSSNSPIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFG 57 (70)
T ss_dssp EEE-STS-HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTS
T ss_pred EEECCCCCHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhc
Confidence 45666666677788888888 889999999999999999999999999985
No 31
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=21.11 E-value=1.1e+02 Score=22.07 Aligned_cols=22 Identities=9% Similarity=0.215 Sum_probs=19.5
Q ss_pred EEecCCChhhHHHHHHHHHHHc
Q 042428 36 VFCKPSKPGQINEFAEEIARLS 57 (106)
Q Consensus 36 I~~~~~~~~~~~e~ae~Le~~s 57 (106)
|+|.+++..+++.+|+.+..+.
T Consensus 38 VIatg~s~rhv~Aiad~i~~~~ 59 (115)
T COG0799 38 VIATGNSSRHVKAIADNVKEEL 59 (115)
T ss_pred EEEEeCchHHHHHHHHHHHHHH
Confidence 7899999999999999998663
No 32
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=20.68 E-value=2e+02 Score=22.58 Aligned_cols=55 Identities=15% Similarity=-0.042 Sum_probs=37.1
Q ss_pred cceeEEEecCCC-hhhHHHHHHHHHHHcCCCC--------CccEEEEecCCCCCCCccccccCCC
Q 042428 31 HEIVKVFCKPSK-PGQINEFAEEIARLSVPPP--------GVDVWLPSDSLGTAFPQVDIEDAGL 86 (106)
Q Consensus 31 rElVKI~~~~~~-~~~~~e~ae~Le~~sGGiv--------gg~~ii~yRgknY~~P~~~~~~~~~ 86 (106)
-+||.+.-.... ...++++++.|+. .+-.. ..+.-+..+++||..|...+-..++
T Consensus 122 ~~lv~~~~~~~~~~~kTK~~~~~lk~-l~~~~~~~l~~~~~~~~n~~ls~Rnl~~~~~~~~~~~~ 185 (214)
T COG0088 122 GKLVVVRGHVFEDAPKTKELVEFLKK-LGLDVKRLLIVKGERDGNGKLSARNLKNVKVVLVVGGL 185 (214)
T ss_pred CCEEEEecccccCCccHHHHHHHHHH-hhhhhceeEEeecccccceeecccCCCCceeeeeeccc
Confidence 367777666555 5668888888887 33222 2345678899999999876665543
No 33
>COG5616 Predicted integral membrane protein [Function unknown]
Probab=20.19 E-value=1.6e+02 Score=22.38 Aligned_cols=39 Identities=18% Similarity=0.322 Sum_probs=27.4
Q ss_pred CccchhHHHHHHHhhhhcceeEE-----EecCCChhhHHHHHHHHHH
Q 042428 14 RRVFGGVILNMHMHWKKHEIVKV-----FCKPSKPGQINEFAEEIAR 55 (106)
Q Consensus 14 rGVf~gVIeniH~hWK~rElVKI-----~~~~~~~~~~~e~ae~Le~ 55 (106)
+|+|+++|.++- |.+|+.-| ...+..+.++++++++|.-
T Consensus 46 DGlTEdiIt~Ls---r~~~l~VIArnssft~kgka~dv~~v~~~Lgv 89 (152)
T COG5616 46 DGLTEDIITDLS---RFRELFVIARNSSFTYKGKAVDVREVGEELGV 89 (152)
T ss_pred ccchHHHHHHhh---hccCceEEEccceeeccCCCCCHHHHHHHhCC
Confidence 789999988887 33555433 2334577899999998864
Done!