Query 043054
Match_columns 90
No_of_seqs 108 out of 232
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 12:22:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043054.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043054hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0857 60s ribosomal protein 100.0 4.5E-30 9.7E-35 194.9 6.2 79 2-80 133-211 (212)
2 PTZ00173 60S ribosomal protein 100.0 8.9E-29 1.9E-33 188.0 7.1 77 5-81 135-211 (213)
3 TIGR00279 L10e ribosomal prote 98.0 4.7E-06 1E-10 62.2 3.3 37 7-43 134-170 (172)
4 PRK04199 rpl10e 50S ribosomal 97.5 9E-05 1.9E-09 55.3 3.2 34 7-40 134-167 (172)
5 COG0197 RplP Ribosomal protein 97.1 0.00025 5.5E-09 51.9 2.0 34 9-45 110-145 (146)
6 PRK09203 rplP 50S ribosomal pr 96.5 0.0024 5.2E-08 45.6 2.9 26 13-38 109-134 (138)
7 cd01433 Ribosomal_L16_L10e Rib 92.1 0.11 2.4E-06 35.2 2.0 22 15-36 91-112 (112)
8 PF00252 Ribosomal_L16: Riboso 91.9 0.14 2.9E-06 36.1 2.4 24 13-36 109-132 (133)
9 CHL00044 rpl16 ribosomal prote 91.4 0.2 4.3E-06 35.8 2.7 24 14-37 110-133 (135)
10 TIGR01164 rplP_bact ribosomal 88.3 0.32 6.9E-06 34.3 1.7 19 13-31 108-126 (126)
11 PRK06770 hypothetical protein; 79.0 0.87 1.9E-05 34.6 0.8 40 13-57 67-106 (180)
12 PRK15458 tagatose 6-phosphate 50.7 25 0.00054 29.9 4.0 42 14-57 25-73 (426)
13 TIGR02810 agaZ_gatZ D-tagatose 49.4 27 0.00059 29.6 4.0 42 14-57 21-69 (420)
14 PRK00075 cbiD cobalt-precorrin 41.9 11 0.00023 31.0 0.5 41 4-44 175-237 (361)
15 PF11504 Colicin_Ia: Colicin I 36.9 17 0.00038 23.7 0.8 16 26-41 12-31 (72)
16 KOG3422 Mitochondrial ribosoma 36.1 35 0.00076 26.8 2.5 30 11-40 149-178 (221)
17 PF13541 ChlI: Subunit ChlI of 35.0 30 0.00065 24.0 1.9 27 13-40 24-50 (121)
18 TIGR01357 aroB 3-dehydroquinat 34.0 70 0.0015 24.9 3.9 31 13-43 297-327 (344)
19 PF12434 Malate_DH: Malate deh 32.5 37 0.0008 18.8 1.6 18 10-27 5-22 (28)
20 cd03775 MATH_Ubp21p Ubiquitin- 32.2 31 0.00067 23.1 1.5 31 38-68 96-130 (134)
21 cd03773 MATH_TRIM37 Tripartite 31.9 28 0.00061 22.8 1.3 29 38-68 96-126 (132)
22 PF13353 Fer4_12: 4Fe-4S singl 31.5 51 0.0011 21.4 2.4 50 14-64 68-117 (139)
23 KOG4603 TBP-1 interacting prot 30.8 50 0.0011 25.6 2.6 41 15-55 39-85 (201)
24 PHA01632 hypothetical protein 30.7 26 0.00057 22.6 0.9 18 26-43 46-63 (64)
25 PHA02957 hypothetical protein; 29.6 31 0.00066 26.4 1.3 30 31-60 118-147 (206)
26 COG2193 Bfr Bacterioferritin ( 29.3 21 0.00045 26.8 0.3 19 39-57 33-51 (157)
27 cd03772 MATH_HAUSP Herpesvirus 29.1 35 0.00075 22.9 1.4 29 39-67 98-126 (137)
28 PF13282 DUF4070: Domain of un 28.7 28 0.00061 24.7 0.9 13 50-62 3-15 (146)
29 PRK13677 hypothetical protein; 28.5 33 0.00072 24.8 1.2 16 26-41 47-62 (125)
30 cd03774 MATH_SPOP Speckle-type 28.4 38 0.00082 22.7 1.5 26 39-64 102-127 (139)
31 COG4208 CysW ABC-type sulfate 27.7 35 0.00075 27.7 1.3 17 19-35 87-103 (287)
32 PRK15052 D-tagatose-1,6-bispho 27.6 1.1E+02 0.0023 26.2 4.2 42 14-57 22-70 (421)
33 KOG1575 Voltage-gated shaker-l 27.1 63 0.0014 26.5 2.7 18 28-45 82-100 (336)
34 PF09419 PGP_phosphatase: Mito 26.4 86 0.0019 23.0 3.1 33 13-45 59-91 (168)
35 KOG4616 Mitochondrial ribosoma 26.0 47 0.001 24.1 1.6 34 42-76 45-78 (137)
36 PF14306 PUA_2: PUA-like domai 25.7 44 0.00096 24.3 1.5 32 33-65 30-75 (160)
37 cd07895 Adenylation_mRNA_cappi 25.2 89 0.0019 22.6 3.0 38 24-70 17-57 (215)
38 PF09288 UBA_3: Fungal ubiquit 24.6 53 0.0011 20.6 1.5 14 15-28 23-36 (55)
39 PF11944 DUF3461: Protein of u 24.4 40 0.00086 24.4 1.0 14 26-39 47-60 (125)
40 PF03720 UDPG_MGDP_dh_C: UDP-g 23.3 72 0.0016 20.8 2.0 37 31-67 66-103 (106)
41 PF01888 CbiD: CbiD; InterPro 22.6 20 0.00044 28.3 -0.8 41 4-44 172-234 (261)
42 KOG1227 Putative methyltransfe 21.4 52 0.0011 27.5 1.3 11 15-25 227-237 (351)
43 KOG2950 Uncharacterized protei 21.1 88 0.0019 26.1 2.5 47 25-72 274-330 (348)
44 PF07747 MTH865: MTH865-like f 21.0 63 0.0014 21.3 1.4 14 15-30 4-17 (75)
45 PF06969 HemN_C: HemN C-termin 20.0 80 0.0017 18.5 1.6 57 13-74 6-64 (66)
No 1
>KOG0857 consensus 60s ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=4.5e-30 Score=194.95 Aligned_cols=79 Identities=43% Similarity=0.691 Sum_probs=74.9
Q ss_pred CccccccccCCCChhHHHHHHhhhccCCCCcceEEeeccccccccChHHHHhhhhcCeeecCCCeEEEeCCCCCCCCCC
Q 043054 2 GLGLVNPIPSRPIANPTQEALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLADRQ 80 (90)
Q Consensus 2 ~~~~~~~~~k~~~~~~viEALRRAKfKFPGRQKI~vSkkWGFTk~~r~ey~~~~~eg~Li~dG~~vk~i~~~GPL~~~~ 80 (90)
|.=+..+++|++|++|+|||||||||||||+|||+||++||||+|++|||++|..++++++|||+|+|++.+|||++|.
T Consensus 133 Gqvi~Svrtk~~nkeh~ieal~rak~kfpG~qki~vs~kwgftk~~~def~~~~~~~~~~~~g~~vk~~~~~gp~~~~~ 211 (212)
T KOG0857|consen 133 GQVIMSVRTKLQNKEHVIEALRRAKFKFPGRQKIVVSKKWGFTKFDRDEFEDLRARKRLEPDGCGVKFIPVCGPLQAII 211 (212)
T ss_pred CceEEEeecCcccHHHHHHHHHhccccCCCceeEEeeeecCccccchhHHHHHHhhcceeccCCceeeecccCchhhcc
Confidence 3344578999999999999999999999999999999999999999999999999999999999999999999999885
No 2
>PTZ00173 60S ribosomal protein L10; Provisional
Probab=99.95 E-value=8.9e-29 Score=188.00 Aligned_cols=77 Identities=43% Similarity=0.796 Sum_probs=73.4
Q ss_pred ccccccCCCChhHHHHHHhhhccCCCCcceEEeeccccccccChHHHHhhhhcCeeecCCCeEEEeCCCCCCCCCCC
Q 043054 5 LVNPIPSRPIANPTQEALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLADRQP 81 (90)
Q Consensus 5 ~~~~~~k~~~~~~viEALRRAKfKFPGRQKI~vSkkWGFTk~~r~ey~~~~~eg~Li~dG~~vk~i~~~GPL~~~~~ 81 (90)
|.....++++.++|+||||||++|||++|||++|++||||+|+++||++|+++|+|++|||+|+++++||||++|..
T Consensus 135 ifei~~~~~~~~~AkeALrrA~~KlP~~~kIv~~~~wgft~~~~~~~~~~~~~~~~~~~g~~~~~~~~~g~l~~~~~ 211 (213)
T PTZ00173 135 LLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFTNYTREEYQKLRAEGKLIQDGVHVKLISPKGPLTKVNP 211 (213)
T ss_pred EEEEecccCCHHHHHHHHHHhcccCCCeEEEEEecccCccccCHHHHHHHHHCCeEecCCceEEEeCCCCChhhhhc
Confidence 45567889999999999999999999999999999999999999999999999999999999999999999999964
No 3
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=98.01 E-value=4.7e-06 Score=62.18 Aligned_cols=37 Identities=35% Similarity=0.594 Sum_probs=33.0
Q ss_pred ccccCCCChhHHHHHHhhhccCCCCcceEEeeccccc
Q 043054 7 NPIPSRPIANPTQEALRRAKFKFPVRQKIIVSRKWGF 43 (90)
Q Consensus 7 ~~~~k~~~~~~viEALRRAKfKFPGRQKI~vSkkWGF 43 (90)
.....+++.++|.||||+|.+|+|++++|+++++|+.
T Consensus 134 ei~~~~~~~~~AkeAlr~A~~KLP~~~kiv~~~~~~~ 170 (172)
T TIGR00279 134 SVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWEL 170 (172)
T ss_pred EEEeecCCHHHHHHHHHHHhccCCCcEEEEEecCccc
Confidence 3445677999999999999999999999999999985
No 4
>PRK04199 rpl10e 50S ribosomal protein L10e; Reviewed
Probab=97.50 E-value=9e-05 Score=55.33 Aligned_cols=34 Identities=29% Similarity=0.407 Sum_probs=29.6
Q ss_pred ccccCCCChhHHHHHHhhhccCCCCcceEEeecc
Q 043054 7 NPIPSRPIANPTQEALRRAKFKFPVRQKIIVSRK 40 (90)
Q Consensus 7 ~~~~k~~~~~~viEALRRAKfKFPGRQKI~vSkk 40 (90)
......++.++|.||||+|.+|+|.+++|+++++
T Consensus 134 ei~~~~~~~~~akeAlr~a~~KLP~k~kiv~~~~ 167 (172)
T PRK04199 134 TVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKG 167 (172)
T ss_pred EEEecCCCHHHHHHHHHHhhccCCCcEEEEEecc
Confidence 3444577999999999999999999999998875
No 5
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=97.14 E-value=0.00025 Score=51.87 Aligned_cols=34 Identities=32% Similarity=0.304 Sum_probs=27.7
Q ss_pred ccCCCChhHHHHHHhhhccCCCCc--ceEEeeccccccc
Q 043054 9 IPSRPIANPTQEALRRAKFKFPVR--QKIIVSRKWGFTK 45 (90)
Q Consensus 9 ~~k~~~~~~viEALRRAKfKFPGR--QKI~vSkkWGFTk 45 (90)
...+.+. |.||||||.+|||++ ++|.++. |.++.
T Consensus 110 ~g~~e~~--A~EAlr~Aa~KLP~~~~~v~~~~~-~~~~~ 145 (146)
T COG0197 110 AGVPEEL--AREALRRAAAKLPVKTKFVIRIEK-REGTE 145 (146)
T ss_pred ecCcHHH--HHHHHHHHhhcCCCceEEEEEEec-chhcc
Confidence 3344444 999999999999999 9999998 87764
No 6
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=96.51 E-value=0.0024 Score=45.62 Aligned_cols=26 Identities=31% Similarity=0.428 Sum_probs=24.1
Q ss_pred CChhHHHHHHhhhccCCCCcceEEee
Q 043054 13 PIANPTQEALRRAKFKFPVRQKIIVS 38 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~vS 38 (90)
.+.++|.|||++|.+|+|++++|++.
T Consensus 109 ~~~~~a~~al~~a~~KLP~~~kii~~ 134 (138)
T PRK09203 109 VSEELAREALRLAAAKLPIKTKFVKR 134 (138)
T ss_pred CCHHHHHHHHHHHhccCCCcEEEEEe
Confidence 68899999999999999999999864
No 7
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=92.11 E-value=0.11 Score=35.25 Aligned_cols=22 Identities=45% Similarity=0.730 Sum_probs=20.4
Q ss_pred hhHHHHHHhhhccCCCCcceEE
Q 043054 15 ANPTQEALRRAKFKFPVRQKII 36 (90)
Q Consensus 15 ~~~viEALRRAKfKFPGRQKI~ 36 (90)
.+.|.|||++|.+|+|.+++++
T Consensus 91 ~~~~~~alk~a~~Klp~~~k~i 112 (112)
T cd01433 91 EEVAKEALRRAAKKLPIKTKIV 112 (112)
T ss_pred HHHHHHHHHHhhccCCCcEEEC
Confidence 8999999999999999998874
No 8
>PF00252 Ribosomal_L16: Ribosomal protein L16p/L10e; InterPro: IPR016180 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a structural domain with an alpha/beta-hammerhead fold, where the beta-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2ZJR_J 1Y69_K 3DLL_J 2ZJQ_J 2ZJP_J 3PIO_J 3CF5_J 3PIP_J 2ZKR_h 3J11_O ....
Probab=91.91 E-value=0.14 Score=36.05 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=22.4
Q ss_pred CChhHHHHHHhhhccCCCCcceEE
Q 043054 13 PIANPTQEALRRAKFKFPVRQKII 36 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~ 36 (90)
-+.+.|.|||++|.+|+|++.+|+
T Consensus 109 v~~~~a~~alk~a~~KLP~~~~~v 132 (133)
T PF00252_consen 109 VNEEEAKEALKRAAKKLPIKTKFV 132 (133)
T ss_dssp SCHHHHHHHHHHHHHTSSSCEEEE
T ss_pred CCHHHHHHHHHHHHhhCCCCEEEe
Confidence 488999999999999999999987
No 9
>CHL00044 rpl16 ribosomal protein L16
Probab=91.35 E-value=0.2 Score=35.77 Aligned_cols=24 Identities=21% Similarity=0.537 Sum_probs=21.4
Q ss_pred ChhHHHHHHhhhccCCCCcceEEe
Q 043054 14 IANPTQEALRRAKFKFPVRQKIIV 37 (90)
Q Consensus 14 ~~~~viEALRRAKfKFPGRQKI~v 37 (90)
+..+|.|||++|..|+|.+-+|+.
T Consensus 110 ~~~~ak~al~~a~~KLP~k~~~v~ 133 (135)
T CHL00044 110 SETIARAAIKIAAYKMPIKTQFII 133 (135)
T ss_pred CHHHHHHHHHHHhhcCCCcEEEEe
Confidence 357899999999999999998875
No 10
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=88.26 E-value=0.32 Score=34.25 Aligned_cols=19 Identities=32% Similarity=0.394 Sum_probs=17.5
Q ss_pred CChhHHHHHHhhhccCCCC
Q 043054 13 PIANPTQEALRRAKFKFPV 31 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPG 31 (90)
.+.++|.|||++|.+|+|.
T Consensus 108 ~~~~~a~~al~~a~~KLP~ 126 (126)
T TIGR01164 108 VPEEVAREAFRLAASKLPI 126 (126)
T ss_pred CCHHHHHHHHHHHHhcCCC
Confidence 6889999999999999994
No 11
>PRK06770 hypothetical protein; Provisional
Probab=78.99 E-value=0.87 Score=34.57 Aligned_cols=40 Identities=18% Similarity=0.413 Sum_probs=32.7
Q ss_pred CChhHHHHHHhhhccCCCCcceEEeeccccccccChHHHHhhhhc
Q 043054 13 PIANPTQEALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSE 57 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~vSkkWGFTk~~r~ey~~~~~e 57 (90)
.....++.|+..- -+||+.-++||||+..+.+.-+.+++.
T Consensus 67 ~tE~~ii~~MH~M-----tHQKV~A~~KwG~~~mT~enI~~l~~~ 106 (180)
T PRK06770 67 STEEEIITAMHKM-----THQKVKADEKWGFIEMTQENIEKLKDI 106 (180)
T ss_pred cCHHHHHHHHHHH-----HhhhhhhhcccceEecCHHHHHHHHHH
Confidence 3566777777664 379999999999999999999888654
No 12
>PRK15458 tagatose 6-phosphate aldolase subunit KbaZ; Provisional
Probab=50.66 E-value=25 Score=29.91 Aligned_cols=42 Identities=24% Similarity=0.225 Sum_probs=29.0
Q ss_pred ChhHHHHH-HhhhccC-CCCcceEEeec-----cccccccChHHHHhhhhc
Q 043054 14 IANPTQEA-LRRAKFK-FPVRQKIIVSR-----KWGFTKFSRADYLRWNSE 57 (90)
Q Consensus 14 ~~~~viEA-LRRAKfK-FPGRQKI~vSk-----kWGFTk~~r~ey~~~~~e 57 (90)
.-+.|||| |++|+=+ +| --|.-|. .-|+|.++..+|.+...+
T Consensus 25 ahp~VieAAl~~a~~~~~p--vLiEAT~NQVnq~GGYTGmtP~dF~~~V~~ 73 (426)
T PRK15458 25 AHPLVLEAAIRYALANDSP--LLIEATSNQVDQFGGYTGMTPADFRGFVCQ 73 (426)
T ss_pred CCHHHHHHHHHHHhhcCCc--EEEEeccccccccCCcCCCCHHHHHHHHHH
Confidence 34567888 9999753 22 2233232 249999999999998877
No 13
>TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit. Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, required both for full activity and for good stability of the aldolase. Note that members of this protein family appear in public databases annotated as putative tagatose 6-phosphate kinases, possibly in error.
Probab=49.44 E-value=27 Score=29.64 Aligned_cols=42 Identities=26% Similarity=0.306 Sum_probs=29.1
Q ss_pred ChhHHHHH-HhhhccC-CCCcceEEeec-----cccccccChHHHHhhhhc
Q 043054 14 IANPTQEA-LRRAKFK-FPVRQKIIVSR-----KWGFTKFSRADYLRWNSE 57 (90)
Q Consensus 14 ~~~~viEA-LRRAKfK-FPGRQKI~vSk-----kWGFTk~~r~ey~~~~~e 57 (90)
.-+.|||| |++||=+ +| --|.-|. .-|+|.++..+|.+...+
T Consensus 21 ahp~VieAAl~~a~~~~~p--vLiEAT~NQVnq~GGYTGmtP~dF~~~V~~ 69 (420)
T TIGR02810 21 AHPLVLEAAIRRARASGTP--VLIEATSNQVNQFGGYTGMTPADFRDFVET 69 (420)
T ss_pred CCHHHHHHHHHHHhhcCCc--EEEEeccccccccCCcCCCCHHHHHHHHHH
Confidence 34567888 9999753 33 2233333 249999999999998877
No 14
>PRK00075 cbiD cobalt-precorrin-6A synthase; Reviewed
Probab=41.89 E-value=11 Score=31.05 Aligned_cols=41 Identities=20% Similarity=0.281 Sum_probs=33.4
Q ss_pred cccccccCCCChhHHHHHHhhh----------------------ccCCCCcceEEeecccccc
Q 043054 4 GLVNPIPSRPIANPTQEALRRA----------------------KFKFPVRQKIIVSRKWGFT 44 (90)
Q Consensus 4 ~~~~~~~k~~~~~~viEALRRA----------------------KfKFPGRQKI~vSkkWGFT 44 (90)
|+|.|.+.+..++++..+|+.| .+.+|-.|-|.+|+.+||+
T Consensus 175 GiV~P~S~~a~~~si~~~l~va~a~g~~~vvl~~G~~ge~~a~~~~~l~~~~~V~~gnfiG~~ 237 (361)
T PRK00075 175 GIVEPMSEEAYLASIKQELDVARANGLDHVVLVTGNNGEDYARKLLGLPEDAIIKMGNFVGPM 237 (361)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHHcCCCeEEEccChHHHHHHHHhcCCChhhEEEeehhHHHH
Confidence 7888888888888888777643 4678888999999999973
No 15
>PF11504 Colicin_Ia: Colicin Ia; InterPro: IPR014740 Colicins are plasmid-encoded polypeptide toxins produced by and active against Escherichia coli and closely related bacteria. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis. Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy []. These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane []. This entry represents the central receptor recognition domain, which has an alpha/beta two-layer sandwich structure.; GO: 0019835 cytolysis, 0050829 defense response to Gram-negative bacterium, 0016021 integral to membrane; PDB: 2HDI_B 1CII_A.
Probab=36.86 E-value=17 Score=23.72 Aligned_cols=16 Identities=44% Similarity=0.420 Sum_probs=9.4
Q ss_pred ccCCCCcc----eEEeeccc
Q 043054 26 KFKFPVRQ----KIIVSRKW 41 (90)
Q Consensus 26 KfKFPGRQ----KI~vSkkW 41 (90)
--|||||. +|+||--=
T Consensus 12 pekfpgrsstn~~i~vsg~~ 31 (72)
T PF11504_consen 12 PEKFPGRSSTNHSIFVSGDP 31 (72)
T ss_dssp TTTS-EEEEEEEEEEE-S-T
T ss_pred cccCCCCCCCCceEEEcCCC
Confidence 35899995 68888543
No 16
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=36.10 E-value=35 Score=26.83 Aligned_cols=30 Identities=17% Similarity=0.277 Sum_probs=26.1
Q ss_pred CCCChhHHHHHHhhhccCCCCcceEEeecc
Q 043054 11 SRPIANPTQEALRRAKFKFPVRQKIIVSRK 40 (90)
Q Consensus 11 k~~~~~~viEALRRAKfKFPGRQKI~vSkk 40 (90)
-|.+.+.|.+||.-|.+|+|+.-+++++..
T Consensus 149 G~~~~~~Ar~al~~aa~klp~~~efVs~~~ 178 (221)
T KOG3422|consen 149 GDVEEEEARQALLQAAHKLPFKYEFVSEEM 178 (221)
T ss_pred CcccHHHHHHHHHHHHhcCCccEEEeeHhh
Confidence 457889999999999999999999887653
No 17
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=35.04 E-value=30 Score=24.00 Aligned_cols=27 Identities=30% Similarity=0.468 Sum_probs=22.2
Q ss_pred CChhHHHHHHhhhccCCCCcceEEeecc
Q 043054 13 PIANPTQEALRRAKFKFPVRQKIIVSRK 40 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~vSkk 40 (90)
+.++.+.-||+-+.|+|| .|+|+|.=.
T Consensus 24 esr~Rv~~al~~~g~~~p-~~~i~VNla 50 (121)
T PF13541_consen 24 ESRERVRSALKNSGFPFP-NQDITVNLA 50 (121)
T ss_pred HHHHHHHHHHHhcCCCCC-cceeeeEEE
Confidence 356889999999999999 578887643
No 18
>TIGR01357 aroB 3-dehydroquinate synthase. This model represents 3-dehydroquinate synthase, the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids.
Probab=33.96 E-value=70 Score=24.86 Aligned_cols=31 Identities=10% Similarity=0.004 Sum_probs=27.7
Q ss_pred CChhHHHHHHhhhccCCCCcceEEeeccccc
Q 043054 13 PIANPTQEALRRAKFKFPVRQKIIVSRKWGF 43 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~vSkkWGF 43 (90)
-..+.++|||+.+|..=+|++++.+-...|=
T Consensus 297 ~~~~~~~~~l~~dkk~~~~~~~~~l~~~iG~ 327 (344)
T TIGR01357 297 LDVDELLNAMLNDKKNSGGKIRFVLLEEIGK 327 (344)
T ss_pred CCHHHHHHHHHHhhhccCCcEEEEEecCCcc
Confidence 4679999999999999999999999988764
No 19
>PF12434 Malate_DH: Malate dehydrogenase enzyme
Probab=32.50 E-value=37 Score=18.83 Aligned_cols=18 Identities=17% Similarity=0.246 Sum_probs=14.7
Q ss_pred cCCCChhHHHHHHhhhcc
Q 043054 10 PSRPIANPTQEALRRAKF 27 (90)
Q Consensus 10 ~k~~~~~~viEALRRAKf 27 (90)
+...+++...++||+|-.
T Consensus 5 s~~d~~~~~r~~lR~AAL 22 (28)
T PF12434_consen 5 STADNKEDKRAQLRQAAL 22 (28)
T ss_pred ccccchHHHHHHHHHHHH
Confidence 566778889999999954
No 20
>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.
Probab=32.17 E-value=31 Score=23.15 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=20.1
Q ss_pred eccccccccChHHHHh----hhhcCeeecCCCeEE
Q 043054 38 SRKWGFTKFSRADYLR----WNSENRIVPDGMNAK 68 (90)
Q Consensus 38 SkkWGFTk~~r~ey~~----~~~eg~Li~dG~~vk 68 (90)
+..|||.+|-+.+..+ -.+.|.|+.|-..+.
T Consensus 96 ~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~ 130 (134)
T cd03775 96 DKDWGFTRFIELRKLAHRTPDKPSPFLENGELNIT 130 (134)
T ss_pred CCCCChhHcccHHHHcccccCCCCceeECCEEEEE
Confidence 4679999996544433 235788887755444
No 21
>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i
Probab=31.88 E-value=28 Score=22.83 Aligned_cols=29 Identities=28% Similarity=0.649 Sum_probs=19.7
Q ss_pred eccccccccChHHHHhhhhcCeeec--CCCeEE
Q 043054 38 SRKWGFTKFSRADYLRWNSENRIVP--DGMNAK 68 (90)
Q Consensus 38 SkkWGFTk~~r~ey~~~~~eg~Li~--dG~~vk 68 (90)
+..|||.+|-+-+. |.++|.|.. |-..++
T Consensus 96 ~~~wG~~~Fi~~~~--L~~~gfl~~~~D~l~i~ 126 (132)
T cd03773 96 GECWGYNRFFRLDL--LINEGYLLPENDTLILR 126 (132)
T ss_pred CCCcCHHHhccHHH--HhhCCCcCCCCCEEEEE
Confidence 35699999877554 446888887 654443
No 22
>PF13353 Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A 3CB8_A 3T7V_A 2YX0_A 3CAN_A.
Probab=31.46 E-value=51 Score=21.44 Aligned_cols=50 Identities=22% Similarity=0.255 Sum_probs=32.8
Q ss_pred ChhHHHHHHhhhccCCCCcceEEeeccccccccChHHHHhhhhcCeeecCC
Q 043054 14 IANPTQEALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDG 64 (90)
Q Consensus 14 ~~~~viEALRRAKfKFPGRQKI~vSkkWGFTk~~r~ey~~~~~eg~Li~dG 64 (90)
+.+.+.+.++.+|=+++ ...++.|+-..+......+..++...-.+.-||
T Consensus 68 ~~~~l~~i~~~~k~~~~-~~~~~~tng~~~~~~~~~~~~~~~~~~~vsvd~ 117 (139)
T PF13353_consen 68 NYDELLEILKYIKEKFP-KKIIILTNGYTLDELLDELIEELLDEIDVSVDG 117 (139)
T ss_dssp SHHHHHHHHHHHHHTT--SEEEEEETT--HHHHHHHHHHHHHHTESEEEE-
T ss_pred cHhHHHHHHHHHHHhCC-CCeEEEECCCchhHHHhHHHHhccCccEEEEEE
Confidence 56889999999999999 667888887777666655555655554444443
No 23
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=30.83 E-value=50 Score=25.56 Aligned_cols=41 Identities=22% Similarity=0.191 Sum_probs=32.3
Q ss_pred hhHHHHHHhh------hccCCCCcceEEeeccccccccChHHHHhhh
Q 043054 15 ANPTQEALRR------AKFKFPVRQKIIVSRKWGFTKFSRADYLRWN 55 (90)
Q Consensus 15 ~~~viEALRR------AKfKFPGRQKI~vSkkWGFTk~~r~ey~~~~ 55 (90)
+..|+++|-. -++|--|.|||.+-+.-=|...+.+|-..|.
T Consensus 39 ktavqk~Ld~La~~Gki~~K~YGKqKIY~a~QDqF~~~~~eel~~ld 85 (201)
T KOG4603|consen 39 KTAVQKTLDQLAQQGKIKEKMYGKQKIYFADQDQFDMVSDEELQVLD 85 (201)
T ss_pred chHHHHHHHHHHHcCchhHHhccceeeEeecHHhhcCCChHHHHHHh
Confidence 4556666643 3788899999999999999888888887663
No 24
>PHA01632 hypothetical protein
Probab=30.75 E-value=26 Score=22.63 Aligned_cols=18 Identities=28% Similarity=0.519 Sum_probs=14.5
Q ss_pred ccCCCCcceEEeeccccc
Q 043054 26 KFKFPVRQKIIVSRKWGF 43 (90)
Q Consensus 26 KfKFPGRQKI~vSkkWGF 43 (90)
.+==-|.-||.=|+.||.
T Consensus 46 nmie~gk~ki~ds~ewgi 63 (64)
T PHA01632 46 NMIENGKIKILDSKEWGI 63 (64)
T ss_pred HHHhcCceEEeccccccc
Confidence 344479999999999995
No 25
>PHA02957 hypothetical protein; Provisional
Probab=29.57 E-value=31 Score=26.45 Aligned_cols=30 Identities=23% Similarity=0.253 Sum_probs=22.0
Q ss_pred CcceEEeeccccccccChHHHHhhhhcCee
Q 043054 31 VRQKIIVSRKWGFTKFSRADYLRWNSENRI 60 (90)
Q Consensus 31 GRQKI~vSkkWGFTk~~r~ey~~~~~eg~L 60 (90)
|+|||-+---+=-...+||||-+.-+|--|
T Consensus 118 gkqki~liyf~fieavtrddytkitqeitl 147 (206)
T PHA02957 118 GKQKIELIYFFFIEAVTRDDYTKITQEITL 147 (206)
T ss_pred ccEEEEEEEEEEEEEeeccchhhHhhhhhh
Confidence 899998765554556788888887777555
No 26
>COG2193 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]
Probab=29.29 E-value=21 Score=26.77 Aligned_cols=19 Identities=32% Similarity=0.709 Sum_probs=16.0
Q ss_pred ccccccccChHHHHhhhhc
Q 043054 39 RKWGFTKFSRADYLRWNSE 57 (90)
Q Consensus 39 kkWGFTk~~r~ey~~~~~e 57 (90)
+.||||+....+|.+...|
T Consensus 33 ~~WG~~~L~~~~~~esi~E 51 (157)
T COG2193 33 KNWGLTKLAAHEYHESIEE 51 (157)
T ss_pred hCcChHHHHHHHHHHHHHH
Confidence 6899999999999876654
No 27
>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway. It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1
Probab=29.06 E-value=35 Score=22.87 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=19.7
Q ss_pred ccccccccChHHHHhhhhcCeeecCCCeE
Q 043054 39 RKWGFTKFSRADYLRWNSENRIVPDGMNA 67 (90)
Q Consensus 39 kkWGFTk~~r~ey~~~~~eg~Li~dG~~v 67 (90)
..|||.+|-+-+...=.+.|.|+.|.+.+
T Consensus 98 ~~~G~~~fi~~~~L~~~~sgyl~~D~l~I 126 (137)
T cd03772 98 NDWGFSNFMTWSEVTDPEKGFIEDDTITL 126 (137)
T ss_pred CCccchheeEHHHhcCCCCCcEECCEEEE
Confidence 58999998775443323578888876544
No 28
>PF13282 DUF4070: Domain of unknown function (DUF4070)
Probab=28.67 E-value=28 Score=24.75 Aligned_cols=13 Identities=23% Similarity=0.322 Sum_probs=11.1
Q ss_pred HHHhhhhcCeeec
Q 043054 50 DYLRWNSENRIVP 62 (90)
Q Consensus 50 ey~~~~~eg~Li~ 62 (90)
-|.+|++||||+.
T Consensus 3 L~~RL~~EGRLl~ 15 (146)
T PF13282_consen 3 LWDRLEREGRLLG 15 (146)
T ss_pred hHHHHHHhcCCCC
Confidence 3789999999984
No 29
>PRK13677 hypothetical protein; Provisional
Probab=28.49 E-value=33 Score=24.83 Aligned_cols=16 Identities=38% Similarity=0.665 Sum_probs=13.0
Q ss_pred ccCCCCcceEEeeccc
Q 043054 26 KFKFPVRQKIIVSRKW 41 (90)
Q Consensus 26 KfKFPGRQKI~vSkkW 41 (90)
|||||-.+|.+.+..-
T Consensus 47 KFKypRq~K~V~~d~g 62 (125)
T PRK13677 47 KFKYPRQRKTVVADGG 62 (125)
T ss_pred ceeccccceeEEecCC
Confidence 9999999998876543
No 30
>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta
Probab=28.41 E-value=38 Score=22.67 Aligned_cols=26 Identities=35% Similarity=0.705 Sum_probs=16.8
Q ss_pred ccccccccChHHHHhhhhcCeeecCC
Q 043054 39 RKWGFTKFSRADYLRWNSENRIVPDG 64 (90)
Q Consensus 39 kkWGFTk~~r~ey~~~~~eg~Li~dG 64 (90)
..|||.+|-+.+...=..+|.|+.|.
T Consensus 102 ~~wG~~~fi~~~~L~~~~~g~l~dD~ 127 (139)
T cd03774 102 KDWGFKKFIRRDFLLDEANGLLPDDK 127 (139)
T ss_pred CccCHHHeeeHHHhhhhhcccccCCE
Confidence 57999998766544323456776554
No 31
>COG4208 CysW ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism]
Probab=27.67 E-value=35 Score=27.74 Aligned_cols=17 Identities=29% Similarity=0.516 Sum_probs=13.3
Q ss_pred HHHHhhhccCCCCcceE
Q 043054 19 QEALRRAKFKFPVRQKI 35 (90)
Q Consensus 19 iEALRRAKfKFPGRQKI 35 (90)
.-|.--|||.||||+-.
T Consensus 87 ~aAW~iakf~F~Gk~lL 103 (287)
T COG4208 87 AAAWAIARFEFPGKALL 103 (287)
T ss_pred HHHHHHHHccCCchhhh
Confidence 34667789999999864
No 32
>PRK15052 D-tagatose-1,6-bisphosphate aldolase subunit GatZ; Provisional
Probab=27.57 E-value=1.1e+02 Score=26.16 Aligned_cols=42 Identities=19% Similarity=0.086 Sum_probs=29.3
Q ss_pred ChhHHHHH-HhhhccC-CCCcceEEeecc-----ccccccChHHHHhhhhc
Q 043054 14 IANPTQEA-LRRAKFK-FPVRQKIIVSRK-----WGFTKFSRADYLRWNSE 57 (90)
Q Consensus 14 ~~~~viEA-LRRAKfK-FPGRQKI~vSkk-----WGFTk~~r~ey~~~~~e 57 (90)
.-+.|||| |++||=+ +| --|.-|.+ -|+|.++..+|.+...+
T Consensus 22 ahp~VieAAl~~a~~~~~p--vLiEAT~NQVdq~GGYTGmtP~dF~~~V~~ 70 (421)
T PRK15052 22 AHPLVIEAALAFDLNSTRK--VLIEATSNQVNQFGGYTGMTPADFREFVYG 70 (421)
T ss_pred CCHHHHHHHHHHHhhcCCc--EEEEeccccccccCCcCCCCHHHHHHHHHH
Confidence 34567888 9999753 33 22333332 49999999999998877
No 33
>KOG1575 consensus Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion]
Probab=27.10 E-value=63 Score=26.50 Aligned_cols=18 Identities=28% Similarity=0.556 Sum_probs=15.5
Q ss_pred CCCC-cceEEeeccccccc
Q 043054 28 KFPV-RQKIIVSRKWGFTK 45 (90)
Q Consensus 28 KFPG-RQKI~vSkkWGFTk 45 (90)
++|+ |-+|+++.|.||..
T Consensus 82 ~~~~~R~~vviaTK~~~~~ 100 (336)
T KOG1575|consen 82 SRGWRRDKVVIATKFGFDY 100 (336)
T ss_pred hcCCcCCcEEEEEEEeccC
Confidence 4677 88999999999987
No 34
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=26.44 E-value=86 Score=23.04 Aligned_cols=33 Identities=27% Similarity=0.238 Sum_probs=27.7
Q ss_pred CChhHHHHHHhhhccCCCCcceEEeeccccccc
Q 043054 13 PIANPTQEALRRAKFKFPVRQKIIVSRKWGFTK 45 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~vSkkWGFTk 45 (90)
.--+.+.+++++.+--|+..+-++||+.-|=..
T Consensus 59 ~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~ 91 (168)
T PF09419_consen 59 EIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSD 91 (168)
T ss_pred cCCHHHHHHHHHHHHHCCCCeEEEEECCCCccc
Confidence 334678889999999999999999999998655
No 35
>KOG4616 consensus Mitochondrial ribosomal protein L55 [Translation, ribosomal structure and biogenesis]
Probab=25.97 E-value=47 Score=24.12 Aligned_cols=34 Identities=26% Similarity=0.383 Sum_probs=28.6
Q ss_pred cccccChHHHHhhhhcCeeecCCCeEEEeCCCCCC
Q 043054 42 GFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPL 76 (90)
Q Consensus 42 GFTk~~r~ey~~~~~eg~Li~dG~~vk~i~~~GPL 76 (90)
..+++.|.+|..+-.-.-+.|||+... ++-+.|-
T Consensus 45 algki~rrdy~h~y~~kfi~pdgstim-ipaaepr 78 (137)
T KOG4616|consen 45 ALGKIHRRDYCHLYPTKFIQPDGSTIM-IPAAEPR 78 (137)
T ss_pred HHHHHHHHhHHhhcceeEEcCCCCeEe-eeccCcH
Confidence 678899999999999999999999887 5655553
No 36
>PF14306 PUA_2: PUA-like domain; PDB: 1M8P_C 1I2D_B 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2OFX_B 1J70_B 1G8F_A ....
Probab=25.73 E-value=44 Score=24.27 Aligned_cols=32 Identities=28% Similarity=0.475 Sum_probs=21.8
Q ss_pred ceEEeecc----------ccccc----cChHHHHhhhhcCeeecCCC
Q 043054 33 QKIIVSRK----------WGFTK----FSRADYLRWNSENRIVPDGM 65 (90)
Q Consensus 33 QKI~vSkk----------WGFTk----~~r~ey~~~~~eg~Li~dG~ 65 (90)
.+|.+|.. -+|++ ++++||+....+++| +||.
T Consensus 30 p~i~l~~~~~~dleli~~G~fsPL~GFM~~~dy~~V~~~~rL-~~G~ 75 (160)
T PF14306_consen 30 PSIELSKRQLCDLELIANGAFSPLTGFMNEEDYESVLETMRL-PDGT 75 (160)
T ss_dssp EEEEE-HHHHHHHHHHHTTTTTT-SEE--HHHHHHHHHHSBE-TTSS
T ss_pred CeEEeCHHHHHHHHHHhcCCCCCCccccCHHHHHHHHhhCCc-CCCC
Confidence 56777653 24554 569999999999999 6774
No 37
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=25.21 E-value=89 Score=22.61 Aligned_cols=38 Identities=26% Similarity=0.335 Sum_probs=23.4
Q ss_pred hhccCCCCcceEEeeccccccccChHHHHhhhhcCeee---cCCCeEEEe
Q 043054 24 RAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIV---PDGMNAKLF 70 (90)
Q Consensus 24 RAKfKFPGRQKI~vSkkWGFTk~~r~ey~~~~~eg~Li---~dG~~vk~i 70 (90)
.-.--|||.|-+-+|++ .+..+..++.++ .||..+..+
T Consensus 17 ~~~~~FpG~~pvs~~~~---------~~~~~~~~~y~ve~K~DG~R~~l~ 57 (215)
T cd07895 17 WERGGFPGSQPVSFSRK---------NLELLKQNDYFVCEKSDGVRYLLL 57 (215)
T ss_pred cCCCCCCCCCccCccHH---------HHHHHhhCCeEEEEeEcCeEEEEE
Confidence 33567999998876654 444555666554 566554433
No 38
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=24.57 E-value=53 Score=20.59 Aligned_cols=14 Identities=36% Similarity=0.442 Sum_probs=10.2
Q ss_pred hhHHHHHHhhhccC
Q 043054 15 ANPTQEALRRAKFK 28 (90)
Q Consensus 15 ~~~viEALRRAKfK 28 (90)
++.|||||||-.+|
T Consensus 23 ~dkVvevlrrlgik 36 (55)
T PF09288_consen 23 RDKVVEVLRRLGIK 36 (55)
T ss_dssp HHHHHHHHHHS--S
T ss_pred HHHHHHHHHHhCCC
Confidence 56799999998766
No 39
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=24.36 E-value=40 Score=24.44 Aligned_cols=14 Identities=43% Similarity=0.838 Sum_probs=12.0
Q ss_pred ccCCCCcceEEeec
Q 043054 26 KFKFPVRQKIIVSR 39 (90)
Q Consensus 26 KfKFPGRQKI~vSk 39 (90)
|||||-.+|.+...
T Consensus 47 KFKfpRq~K~v~~d 60 (125)
T PF11944_consen 47 KFKFPRQRKTVLVD 60 (125)
T ss_pred ceeccCccceeeec
Confidence 99999999977655
No 40
>PF03720 UDPG_MGDP_dh_C: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; InterPro: IPR014027 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the C-terminal substrate-binding domain of these enzymes. Structural studies indicate that this domain forms an incomplete dinucleotide binding fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3GG2_D 1DLI_A 1DLJ_A 2Y0E_D 2Y0D_B 2Y0C_D 1MV8_B 1MUU_A 1MFZ_C 3TDK_B ....
Probab=23.33 E-value=72 Score=20.77 Aligned_cols=37 Identities=11% Similarity=0.266 Sum_probs=27.0
Q ss_pred CcceEEeeccc-cccccChHHHHhhhhcCeeecCCCeE
Q 043054 31 VRQKIIVSRKW-GFTKFSRADYLRWNSENRIVPDGMNA 67 (90)
Q Consensus 31 GRQKI~vSkkW-GFTk~~r~ey~~~~~eg~Li~dG~~v 67 (90)
|---|++...| .|...+-+++..+...+.+|-|+.++
T Consensus 66 ~~D~vvl~t~h~~f~~l~~~~~~~~~~~~~~iiD~~~~ 103 (106)
T PF03720_consen 66 GADAVVLATDHDEFRELDWEEIAKLMRKPPVIIDGRNI 103 (106)
T ss_dssp TESEEEESS--GGGGCCGHHHHHHHSCSSEEEEESSST
T ss_pred CCCEEEEEecCHHHhccCHHHHHHhcCCCCEEEECccc
Confidence 44557777888 88888888888777788888887654
No 41
>PF01888 CbiD: CbiD; InterPro: IPR002748 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CbiD, an essential protein for cobalamin biosynthesis in both Salmonella typhimurium and Bacillus megaterium. A deletion mutant of CbiD suggests that this enzyme is involved in C-1 methylation and deacylation reactions required during the ring contraction process in the anaerobic pathway to cobalamin (similar role as CobF) []. The CbiD protein has a putative S-AdoMet binding site []. CbiD has no counterpart in the aerobic pathway.; GO: 0016740 transferase activity, 0009236 cobalamin biosynthetic process; PDB: 1SR8_A.
Probab=22.58 E-value=20 Score=28.29 Aligned_cols=41 Identities=17% Similarity=0.382 Sum_probs=17.1
Q ss_pred cccccccCCCChhHHHHHHhhh----------------------ccCCCCcceEEeecccccc
Q 043054 4 GLVNPIPSRPIANPTQEALRRA----------------------KFKFPVRQKIIVSRKWGFT 44 (90)
Q Consensus 4 ~~~~~~~k~~~~~~viEALRRA----------------------KfKFPGRQKI~vSkkWGFT 44 (90)
|+|.|.+.+..++.+...|+-| .|.+|..+-|.+|+-+||+
T Consensus 172 GiV~P~S~~a~~~si~~~i~v~~a~g~~~vvl~~G~~ge~~a~~~~~l~~~~~v~~gnfiG~~ 234 (261)
T PF01888_consen 172 GIVEPMSEEAYKASIRQEIDVARASGCDTVVLVPGNYGEKFARRLLGLPEEAIVQMGNFIGFA 234 (261)
T ss_dssp SEE---SHHHHHHHHHH------GGG-SEEEEESSHHHHHHHHHH-TS--EEEE------TT-
T ss_pred EEEEECCHHHHHhHHhhhhhhhhhCCCCeEEEccChHHHHHHHHhhccchhcEEEecchhHHH
Confidence 6777777777777776655544 3567888888888888874
No 42
>KOG1227 consensus Putative methyltransferase [General function prediction only]
Probab=21.41 E-value=52 Score=27.46 Aligned_cols=11 Identities=45% Similarity=0.392 Sum_probs=9.6
Q ss_pred hhHHHHHHhhh
Q 043054 15 ANPTQEALRRA 25 (90)
Q Consensus 15 ~~~viEALRRA 25 (90)
.++++|||||+
T Consensus 227 Np~svEaLrR~ 237 (351)
T KOG1227|consen 227 NPWSVEALRRN 237 (351)
T ss_pred CHHHHHHHHHH
Confidence 36899999998
No 43
>KOG2950 consensus Uncharacterized protein involved in protein-protein interaction, contains polyproline-binding GYF domain [General function prediction only]
Probab=21.13 E-value=88 Score=26.13 Aligned_cols=47 Identities=11% Similarity=0.278 Sum_probs=33.7
Q ss_pred hccCCCCcceEEeeccccc----c------ccChHHHHhhhhcCeeecCCCeEEEeCC
Q 043054 25 AKFKFPVRQKIIVSRKWGF----T------KFSRADYLRWNSENRIVPDGMNAKLFGC 72 (90)
Q Consensus 25 AKfKFPGRQKI~vSkkWGF----T------k~~r~ey~~~~~eg~Li~dG~~vk~i~~ 72 (90)
+-+--+-|-.-+.+.+|+| | .|+..++..+.++|.. ++|++|+++..
T Consensus 274 ~~~s~~~~~~~~~~~~wefkwe~d~~~~yGp~ts~~m~~w~~egyf-~~~v~~r~~~~ 330 (348)
T KOG2950|consen 274 ESSSDSSRYDNHSEVQWEFKWEFDEDEYYGPYTSSEMQYWQNEGYF-KNAVYVRFHDE 330 (348)
T ss_pred CCccccccccCccceeEeeEeecccccccccccHHHHhhhhccCcc-ccceeEEeecC
Confidence 3344455555556665554 4 6788899999999988 78999998873
No 44
>PF07747 MTH865: MTH865-like family; InterPro: IPR024093 This entry represents a group of uncharacterised hypothetical proteins from archaea, including the 8.4 kDa protein MTH865 from Methanobacterium thermoautotrophicum. The NMR structure of MTH865 reveals an EF-Hand-like fold consisting of four helices in two hairpins [].; PDB: 1IIO_A.
Probab=20.95 E-value=63 Score=21.32 Aligned_cols=14 Identities=36% Similarity=0.577 Sum_probs=12.0
Q ss_pred hhHHHHHHhhhccCCC
Q 043054 15 ANPTQEALRRAKFKFP 30 (90)
Q Consensus 15 ~~~viEALRRAKfKFP 30 (90)
+.+++|||+-|+ ||
T Consensus 4 k~qi~~a~~~a~--FP 17 (75)
T PF07747_consen 4 KAQIVEAFKGAD--FP 17 (75)
T ss_dssp HHHHHHHHTTSS--ST
T ss_pred HHHHHHHHhcCC--CC
Confidence 578899999998 77
No 45
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=20.04 E-value=80 Score=18.47 Aligned_cols=57 Identities=12% Similarity=0.140 Sum_probs=33.5
Q ss_pred CChhHHHHHHhhhccCCCCcceEEeecccc--ccccChHHHHhhhhcCeeecCCCeEEEeCCCC
Q 043054 13 PIANPTQEALRRAKFKFPVRQKIIVSRKWG--FTKFSRADYLRWNSENRIVPDGMNAKLFGCHG 74 (90)
Q Consensus 13 ~~~~~viEALRRAKfKFPGRQKI~vSkkWG--FTk~~r~ey~~~~~eg~Li~dG~~vk~i~~~G 74 (90)
.-.+.++.+||... |=..-.+.+++| |...-.+....+.++|-+.-++.++. ++.+|
T Consensus 6 ~~~e~i~~~LR~~~----Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~-lT~~G 64 (66)
T PF06969_consen 6 RLREYIMLGLRCNE----GIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGGRLR-LTEKG 64 (66)
T ss_dssp HHHHHHHHHHHHHS----EEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SSEEE-E-TTT
T ss_pred HHHHHHHHHHHhHC----CcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCCEEE-ECccc
Confidence 34567777777751 111112234445 33444677888999999999988877 55555
Done!