Query 037282
Match_columns 56
No_of_seqs 113 out of 767
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 10:38:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037282.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037282hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00218 40S ribosomal protein 100.0 9.4E-33 2E-37 155.2 3.7 53 4-56 2-54 (54)
2 KOG3506 40S ribosomal protein 100.0 2E-31 4.4E-36 150.4 2.1 56 1-56 1-56 (56)
3 PRK05766 rps14P 30S ribosomal 99.9 7.8E-27 1.7E-31 129.9 3.6 51 6-56 2-52 (52)
4 COG0199 RpsN Ribosomal protein 99.9 8.1E-24 1.8E-28 121.2 2.6 48 7-56 10-60 (61)
5 PRK08061 rpsN 30S ribosomal pr 99.8 4.8E-19 1E-23 101.4 3.8 47 7-55 10-59 (61)
6 PF00253 Ribosomal_S14: Riboso 99.8 1E-18 2.2E-23 97.3 4.0 46 9-56 5-55 (55)
7 PRK06911 rpsN 30S ribosomal pr 99.6 1.6E-16 3.4E-21 97.7 2.8 46 8-55 48-98 (100)
8 PRK08881 rpsN 30S ribosomal pr 99.6 8.6E-16 1.9E-20 94.4 2.2 46 8-55 49-99 (101)
9 CHL00074 rps14 ribosomal prote 99.6 1.3E-15 2.9E-20 93.4 2.3 46 8-55 48-98 (100)
10 KOG1741 Mitochondrial/chloropl 99.1 9.8E-12 2.1E-16 77.4 0.5 45 8-54 51-100 (103)
11 PF10764 Gin: Inhibitor of sig 65.4 4.9 0.00011 21.4 1.5 29 21-49 2-31 (46)
12 COG2174 RPL34A Ribosomal prote 63.9 5.7 0.00012 24.5 1.8 32 18-49 34-84 (93)
13 COG2051 RPS27A Ribosomal prote 49.9 6 0.00013 23.1 0.2 21 2-26 26-46 (67)
14 PF13592 HTH_33: Winged helix- 47.7 9.5 0.00021 20.5 0.8 24 31-54 15-38 (60)
15 PRK08359 transcription factor; 46.9 13 0.00029 24.8 1.5 30 19-48 7-42 (176)
16 PF14471 DUF4428: Domain of un 46.6 17 0.00037 19.5 1.7 27 20-46 1-30 (51)
17 PF04981 NMD3: NMD3 family ; 43.8 13 0.00027 25.1 1.1 23 21-47 1-24 (236)
18 PF09607 BrkDBD: Brinker DNA-b 38.7 9 0.00019 21.7 -0.2 21 25-47 26-46 (58)
19 PF04423 Rad50_zn_hook: Rad50 33.8 12 0.00026 19.8 -0.3 8 20-27 22-29 (54)
20 PF01412 ArfGap: Putative GTPa 33.1 37 0.0008 20.5 1.8 28 16-43 11-40 (116)
21 TIGR01623 put_zinc_LRP1 putati 32.3 17 0.00037 19.6 0.2 27 21-49 2-28 (43)
22 PLN00206 DEAD-box ATP-dependen 30.3 35 0.00077 25.3 1.7 22 10-31 20-41 (518)
23 PF00105 zf-C4: Zinc finger, C 26.7 22 0.00049 19.4 0.1 26 20-46 2-30 (70)
24 COG2126 RPL37A Ribosomal prote 26.7 39 0.00085 19.4 1.1 17 16-32 14-30 (61)
25 PF03660 PHF5: PHF5-like prote 26.0 31 0.00066 21.7 0.6 30 14-46 51-80 (106)
26 PRK08298 cytidine deaminase; V 25.7 33 0.00072 21.8 0.7 18 30-49 85-102 (136)
27 cd07165 NR_DBD_DmE78_like DNA- 25.4 36 0.00079 19.5 0.8 20 21-41 1-20 (81)
28 KOG0808 Carbon-nitrogen hydrol 24.4 32 0.0007 25.5 0.5 14 29-42 339-352 (387)
29 PF04405 ScdA_N: Domain of Unk 24.2 20 0.00044 19.6 -0.4 24 28-51 16-42 (56)
30 PTZ00334 trans-sialidase; Prov 23.6 55 0.0012 26.6 1.7 34 14-47 10-48 (780)
31 PF13945 NST1: Salt tolerance 22.8 19 0.00041 24.5 -0.9 15 17-31 140-154 (190)
32 PF14952 zf-tcix: Putative tre 22.0 55 0.0012 17.6 1.0 33 14-48 7-42 (44)
33 COG1997 RPL43A Ribosomal prote 21.8 26 0.00056 21.5 -0.3 26 16-42 33-59 (89)
34 PF10013 DUF2256: Uncharacteri 21.3 39 0.00084 18.0 0.4 11 18-28 8-18 (42)
35 PRK06848 hypothetical protein; 21.0 49 0.0011 21.0 0.8 19 29-49 92-110 (139)
36 cd07168 NR_DBD_DHR4_like DNA-b 20.8 46 0.001 19.5 0.6 22 19-41 7-28 (90)
37 COG1102 Cmk Cytidylate kinase 20.7 48 0.001 22.6 0.8 13 40-52 32-44 (179)
38 COG1499 NMD3 NMD protein affec 20.5 71 0.0015 23.5 1.7 27 16-45 4-30 (355)
39 TIGR00270 conserved hypothetic 20.5 56 0.0012 21.1 1.1 23 21-43 3-31 (154)
40 COG4901 Ribosomal protein S25 20.1 34 0.00073 21.6 -0.1 23 27-49 62-86 (107)
No 1
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=99.97 E-value=9.4e-33 Score=155.16 Aligned_cols=53 Identities=66% Similarity=1.307 Sum_probs=51.8
Q ss_pred ccchhcCCCCCCCccceeeecCCCcceeccCCCchhhHHHHhhhhhcCceeCC
Q 037282 4 SNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56 (56)
Q Consensus 4 ~~~~~~~pr~~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~~Gf~K~~ 56 (56)
.++|++|||++|+++++|.+||+++|+|||||||+|||||||+|.+|||+||+
T Consensus 2 ~~~~~shpr~yGkGsr~C~vCg~~~gliRkygL~~CRqCFRe~A~~iGF~K~~ 54 (54)
T PTZ00218 2 GHLFNTHPRTYGKGSRQCRVCSNRHGLIRKYGLNVCRQCFRENAELIGFHKYR 54 (54)
T ss_pred CccccCCCCcCCCCCCeeecCCCcchhhhhcCcchhhHHHHHhhHhcCeeecC
Confidence 58999999999999999999999999999999999999999999999999996
No 2
>KOG3506 consensus 40S ribosomal protein S29 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2e-31 Score=150.39 Aligned_cols=56 Identities=63% Similarity=1.337 Sum_probs=55.3
Q ss_pred CCcccchhcCCCCCCCccceeeecCCCcceeccCCCchhhHHHHhhhhhcCceeCC
Q 037282 1 MGHSNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56 (56)
Q Consensus 1 m~~~~~~~~~pr~~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~~Gf~K~~ 56 (56)
|||+|+|++||+++|++++.|.+|++.+|+|+|||||+||+||||.|.+|||.||+
T Consensus 1 mgh~~l~~sh~~kfg~GsrsC~vCsn~~gLIrKYGL~vcr~cfr~~a~digf~k~d 56 (56)
T KOG3506|consen 1 MGHQQLWWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNVCRQCFREYANDIGFIKYD 56 (56)
T ss_pred CCcccccccCccccCCCCcceeeeccchhHHHHhhhHHhHHHHHhhccccCCccCC
Confidence 99999999999999999999999999999999999999999999999999999986
No 3
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=99.93 E-value=7.8e-27 Score=129.91 Aligned_cols=51 Identities=47% Similarity=1.008 Sum_probs=47.4
Q ss_pred chhcCCCCCCCccceeeecCCCcceeccCCCchhhHHHHhhhhhcCceeCC
Q 037282 6 VWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56 (56)
Q Consensus 6 ~~~~~pr~~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~~Gf~K~~ 56 (56)
++..+|+++++++|+|.+|||++|||++||||+||+||||+|.+|||+||+
T Consensus 2 ~~~p~~~~~~r~~nrC~~~Gr~rgvirkf~l~lcR~~FRe~A~~~gf~k~~ 52 (52)
T PRK05766 2 YKPPKKRKYGKGARECQRCGRKQGLIRKYGLYLCRQCFREVAPKLGFKKYS 52 (52)
T ss_pred CCCCCCCCCCCCCceeecCCCCceeHHhhCCcccHHHHHHHHHHhCceecC
Confidence 345677788999999999999999999999999999999999999999996
No 4
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=8.1e-24 Score=121.21 Aligned_cols=48 Identities=46% Similarity=0.899 Sum_probs=44.5
Q ss_pred hhcCCCCCCCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCceeCC
Q 037282 7 WNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVKYR 56 (56)
Q Consensus 7 ~~~~pr~~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K~~ 56 (56)
+..+|+.+++++|+|.+||||+||||||+| ||+||||+|++ +||+||+
T Consensus 10 ~~p~~~~~~r~~nRC~~cGRprg~~Rkf~l--cR~cfRE~A~~g~ipGv~K~s 60 (61)
T COG0199 10 ALPRPKSPGRGRNRCRRCGRPRGVIRKFGL--CRICFRELAHKGEIPGVKKAS 60 (61)
T ss_pred cCCCCCccccccccccccCCCccchhhhhh--HHHHHHHHhhccCCCCeEecc
Confidence 455677789999999999999999999999 99999999999 9999985
No 5
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.76 E-value=4.8e-19 Score=101.42 Aligned_cols=47 Identities=40% Similarity=0.754 Sum_probs=43.7
Q ss_pred hhcCCCCCCCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCceeC
Q 037282 7 WNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVKY 55 (56)
Q Consensus 7 ~~~~pr~~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K~ 55 (56)
+.+.||+.++.+|+|.+|||++|+|++||| ||+||||+|.+ +|++|-
T Consensus 10 ~~~~~k~~~r~~nRC~~tGR~rgvir~fgl--~R~~FRe~A~~G~ipGv~Ka 59 (61)
T PRK08061 10 AKRKPKFKVRAYTRCERCGRPHSVYRKFGL--CRICFRELAYKGQIPGVKKA 59 (61)
T ss_pred hhcCCCCCcccceeeecCCCCcceeccCCc--cHHHHHHHHHcCcCCCeeec
Confidence 467899999999999999999999999998 99999999999 898874
No 6
>PF00253 Ribosomal_S14: Ribosomal protein S14p/S29e; InterPro: IPR001209 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 [, ]. S14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins [, ] that include, bacterial, algal and plant chloroplast, yeast mitochondrial, cyanelle and archael, Methanococcus vannielii S14's, as well as yeast mitochondrial MRP2, yeast YS29A/B and mammalian S29.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_N 2XZM_N 1S1H_N 3IZ6_N 2YKR_N 2QBB_N 3I1Z_N 3OAQ_N 3R8O_N 2Z4K_N ....
Probab=99.75 E-value=1e-18 Score=97.33 Aligned_cols=46 Identities=33% Similarity=0.587 Sum_probs=41.7
Q ss_pred cCCCC--CCCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCceeCC
Q 037282 9 SHPKT--YGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVKYR 56 (56)
Q Consensus 9 ~~pr~--~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K~~ 56 (56)
..|++ .++++|+|.+|||++|+|++|+| ||++|||+|.+ +||+|++
T Consensus 5 ~~p~~s~~~r~~nrC~~tGR~rgv~r~f~l--sR~~fR~~a~~g~l~G~~KsS 55 (55)
T PF00253_consen 5 KLPRNSSPTRIKNRCVITGRSRGVIRKFGL--SRICFRELASKGLLPGVKKSS 55 (55)
T ss_dssp SSSSSSSCTGSCSSBSSSCSSSSBETTTSS--BHHHHHHHHHTTSSTTEEES-
T ss_pred hCCCCCCCCCCCeecccCCCceeeeccccc--cHHHHHHHHHcCCCCCEEeCC
Confidence 45555 59999999999999999999999 99999999999 9999974
No 7
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.63 E-value=1.6e-16 Score=97.72 Aligned_cols=46 Identities=35% Similarity=0.626 Sum_probs=43.0
Q ss_pred hcCCCCC--CCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCceeC
Q 037282 8 NSHPKTY--GPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVKY 55 (56)
Q Consensus 8 ~~~pr~~--~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K~ 55 (56)
.++|+++ ++.+|||.+||||+||||+||| ||+.|||+|+. +|.+|-
T Consensus 48 ~~lPrnss~~R~rNRC~~TGR~Rgv~r~FgL--sRi~~Rela~~G~lPGv~Ka 98 (100)
T PRK06911 48 AKLPVNSNPVRYVTRCKQCGRPHAVYRKFNL--CRICLRQQLMVGNIPGGRKS 98 (100)
T ss_pred HhCCCccCcchhhcccCCCCCCcccccccCc--hHHHHHHHHHcCCCCCeecc
Confidence 5789986 9999999999999999999999 99999999999 898874
No 8
>PRK08881 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.57 E-value=8.6e-16 Score=94.35 Aligned_cols=46 Identities=30% Similarity=0.492 Sum_probs=43.0
Q ss_pred hcCCCCC--CCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCceeC
Q 037282 8 NSHPKTY--GPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVKY 55 (56)
Q Consensus 8 ~~~pr~~--~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K~ 55 (56)
..+|+++ ++.+|||.+|||++|+|++||| ||+.|||+|+. +|++|-
T Consensus 49 ~~lPr~ss~tRi~NRC~~TGR~Rgv~r~F~L--sRi~fRela~~G~lpGv~Ks 99 (101)
T PRK08881 49 QKLPRNSSPTRLRNRCELTGRPRGYYRKFGL--SRIKLRELAHRGEIPGVVKA 99 (101)
T ss_pred HhCCcccchHHHhccccCCCCCCccccCcCc--hHHHHHHHHHcCCCCCeecc
Confidence 5789986 9999999999999999999999 99999999999 898874
No 9
>CHL00074 rps14 ribosomal protein S14
Probab=99.56 E-value=1.3e-15 Score=93.45 Aligned_cols=46 Identities=28% Similarity=0.470 Sum_probs=42.9
Q ss_pred hcCCCCC--CCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCceeC
Q 037282 8 NSHPKTY--GPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVKY 55 (56)
Q Consensus 8 ~~~pr~~--~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K~ 55 (56)
.++|+++ ++.+|||.+|||++|||++||| ||+.|||+|.. +|++|-
T Consensus 48 ~~lpr~ss~tRi~NRC~~TGR~Rgv~r~F~L--sRi~~Re~a~~G~ipGv~Ka 98 (100)
T CHL00074 48 QSLPRNSAPTRLHNRCFLTGRPRGNYRDFGL--SRHVLREMAHACLLPGVTKS 98 (100)
T ss_pred HhCCcccchHHHhccccCCCCCCccccCcCc--hHHHHHHHHHcCCCCCcccc
Confidence 6789986 9999999999999999999999 99999999998 898874
No 10
>KOG1741 consensus Mitochondrial/chloroplast ribosomal protein S14/S29 [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=9.8e-12 Score=77.37 Aligned_cols=45 Identities=24% Similarity=0.498 Sum_probs=40.8
Q ss_pred hcCCCCC--CCccceeeecCCCcceeccCCCchhhHHHHhhhhh---cCcee
Q 037282 8 NSHPKTY--GPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKE---IGFVK 54 (56)
Q Consensus 8 ~~~pr~~--~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~A~~---~Gf~K 54 (56)
.++|+++ +++.|+|.-|||++|+++.|+| ||+.|||+|.. +|..|
T Consensus 51 ~alPrns~ptrI~NRCv~TGR~R~v~r~frL--sR~~FR~~A~~~~LpGv~r 100 (103)
T KOG1741|consen 51 QALPRNSAPTRIKNRCVFTGRPRGVYRDFRL--SRHVFRELADAGALPGVTR 100 (103)
T ss_pred hcCccccchHHHHHHHHhcCCcccccchhhh--HHHHHHHHHHhccCcCccc
Confidence 4678885 9999999999999999999999 99999999988 77665
No 11
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=65.43 E-value=4.9 Score=21.45 Aligned_cols=29 Identities=28% Similarity=0.721 Sum_probs=23.0
Q ss_pred eeecCCCcc-eeccCCCchhhHHHHhhhhh
Q 037282 21 CRVCGNPHA-IIRKYGLMCCRQCFRSNAKE 49 (56)
Q Consensus 21 C~~cGr~~g-~irkfgl~~cR~~fRe~A~~ 49 (56)
|.+||.+.. =|.-+|-++|..|=.++..-
T Consensus 2 CiiC~~~~~~GI~I~~~fIC~~CE~~iv~~ 31 (46)
T PF10764_consen 2 CIICGKEKEEGIHIYGKFICSDCEKEIVNT 31 (46)
T ss_pred eEeCCCcCCCCEEEECeEehHHHHHHhccC
Confidence 899999753 45678888999999988753
No 12
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=63.94 E-value=5.7 Score=24.50 Aligned_cols=32 Identities=38% Similarity=0.838 Sum_probs=24.1
Q ss_pred cceeeecCCC-cceecc------------------CCCchhhHHHHhhhhh
Q 037282 18 SRACRVCGNP-HAIIRK------------------YGLMCCRQCFRSNAKE 49 (56)
Q Consensus 18 ~~rC~~cGr~-~g~irk------------------fgl~~cR~~fRe~A~~ 49 (56)
.-+|.+||++ +|+.+. ||=.+|-.|++|+..+
T Consensus 34 ~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~~~i~~ 84 (93)
T COG2174 34 IPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVRERIKR 84 (93)
T ss_pred CCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHHHHHHH
Confidence 4689999997 566554 7766799999887543
No 13
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=49.88 E-value=6 Score=23.06 Aligned_cols=21 Identities=38% Similarity=0.710 Sum_probs=15.5
Q ss_pred CcccchhcCCCCCCCccceeeecCC
Q 037282 2 GHSNVWNSHPKTYGPGSRACRVCGN 26 (56)
Q Consensus 2 ~~~~~~~~~pr~~~r~~~rC~~cGr 26 (56)
+|.++.++||...+ +|.+||+
T Consensus 26 ~N~q~vFshast~V----~C~~CG~ 46 (67)
T COG2051 26 GNEQVVFSHASTVV----TCLICGT 46 (67)
T ss_pred CCEEEEeccCceEE----Eeccccc
Confidence 57778888876554 5888887
No 14
>PF13592 HTH_33: Winged helix-turn helix
Probab=47.67 E-value=9.5 Score=20.55 Aligned_cols=24 Identities=17% Similarity=0.261 Sum_probs=21.0
Q ss_pred eccCCCchhhHHHHhhhhhcCcee
Q 037282 31 IRKYGLMCCRQCFRSNAKEIGFVK 54 (56)
Q Consensus 31 irkfgl~~cR~~fRe~A~~~Gf~K 54 (56)
-+.||+.+++...+.+-+++||..
T Consensus 15 ~~~fgv~ys~~~v~~lL~r~G~s~ 38 (60)
T PF13592_consen 15 EEEFGVKYSPSGVYRLLKRLGFSY 38 (60)
T ss_pred HHHHCCEEcHHHHHHHHHHcCCcc
Confidence 357999999999999999999963
No 15
>PRK08359 transcription factor; Validated
Probab=46.91 E-value=13 Score=24.78 Aligned_cols=30 Identities=27% Similarity=0.800 Sum_probs=22.9
Q ss_pred ceeeecCCC-cce-----eccCCCchhhHHHHhhhh
Q 037282 19 RACRVCGNP-HAI-----IRKYGLMCCRQCFRSNAK 48 (56)
Q Consensus 19 ~rC~~cGr~-~g~-----irkfgl~~cR~~fRe~A~ 48 (56)
..|.+||++ .|. |-.--|++|..|.+.+-.
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G~ 42 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYGR 42 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhCC
Confidence 349999996 454 667778999999977654
No 16
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=46.57 E-value=17 Score=19.52 Aligned_cols=27 Identities=19% Similarity=0.904 Sum_probs=21.2
Q ss_pred eeeecCCCcceeccCCC---chhhHHHHhh
Q 037282 20 ACRVCGNPHAIIRKYGL---MCCRQCFRSN 46 (56)
Q Consensus 20 rC~~cGr~~g~irkfgl---~~cR~~fRe~ 46 (56)
.|.+||..-|++..+.+ ++|-.|+-++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 48999999999884432 6799999776
No 17
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=43.81 E-value=13 Score=25.09 Aligned_cols=23 Identities=35% Similarity=0.947 Sum_probs=16.5
Q ss_pred eeecCCCcc-eeccCCCchhhHHHHhhh
Q 037282 21 CRVCGNPHA-IIRKYGLMCCRQCFRSNA 47 (56)
Q Consensus 21 C~~cGr~~g-~irkfgl~~cR~~fRe~A 47 (56)
|..||++-- ++. || |-.||.+..
T Consensus 1 C~~CG~~~~~~~~--~l--C~~C~~~~~ 24 (236)
T PF04981_consen 1 CPRCGREIEPLID--GL--CPDCYLKRF 24 (236)
T ss_pred CCCCCCCCCCccc--cc--ChHHhcccC
Confidence 889999643 333 55 999998754
No 18
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=38.74 E-value=9 Score=21.66 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=15.4
Q ss_pred CCCcceeccCCCchhhHHHHhhh
Q 037282 25 GNPHAIIRKYGLMCCRQCFRSNA 47 (56)
Q Consensus 25 Gr~~g~irkfgl~~cR~~fRe~A 47 (56)
|+.|+.=|+||+ .|.+.|+.-
T Consensus 26 ~~~RAaarkf~V--~r~~Vr~W~ 46 (58)
T PF09607_consen 26 GNQRAAARKFNV--SRRQVRKWR 46 (58)
T ss_dssp T-HHHHHHHTTS---HHHHHHHH
T ss_pred hhHHHHHHHhCc--cHHHHHHHH
Confidence 456778899999 999998753
No 19
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=33.78 E-value=12 Score=19.78 Aligned_cols=8 Identities=50% Similarity=1.618 Sum_probs=4.5
Q ss_pred eeeecCCC
Q 037282 20 ACRVCGNP 27 (56)
Q Consensus 20 rC~~cGr~ 27 (56)
.|.+|||+
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 89999996
No 20
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=33.09 E-value=37 Score=20.47 Aligned_cols=28 Identities=36% Similarity=1.026 Sum_probs=17.4
Q ss_pred CccceeeecCCCcc--eeccCCCchhhHHH
Q 037282 16 PGSRACRVCGNPHA--IIRKYGLMCCRQCF 43 (56)
Q Consensus 16 r~~~rC~~cGr~~g--~irkfgl~~cR~~f 43 (56)
.+-+.|.-||.+.. +-=.||+++|-.|.
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Ca 40 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLECA 40 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHHHH
Confidence 34478999998653 22379999998886
No 21
>TIGR01623 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.
Probab=32.34 E-value=17 Score=19.56 Aligned_cols=27 Identities=30% Similarity=0.658 Sum_probs=17.9
Q ss_pred eeecCCCcceeccCCCchhhHHHHhhhhh
Q 037282 21 CRVCGNPHAIIRKYGLMCCRQCFRSNAKE 49 (56)
Q Consensus 21 C~~cGr~~g~irkfgl~~cR~~fRe~A~~ 49 (56)
|..||+|.|-==.|.+ ||-|=+..+-|
T Consensus 2 C~~CgNpa~k~C~~~~--CRtCCK~r~~D 28 (43)
T TIGR01623 2 CQDCGNQAKKECLFER--CRTCCKSRGFH 28 (43)
T ss_pred hhhccchhhCCCchhh--hhHHhcccCcC
Confidence 6678887766556666 88776655443
No 22
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=30.33 E-value=35 Score=25.27 Aligned_cols=22 Identities=32% Similarity=0.597 Sum_probs=17.7
Q ss_pred CCCCCCCccceeeecCCCccee
Q 037282 10 HPKTYGPGSRACRVCGNPHAII 31 (56)
Q Consensus 10 ~pr~~~r~~~rC~~cGr~~g~i 31 (56)
-.|.+..+...|.+|||..-||
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~ 41 (518)
T PLN00206 20 EQREALPGEPKCVVCGRYGEYI 41 (518)
T ss_pred HhcCCCCCCceEEEecCcccee
Confidence 3566788889999999987776
No 23
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=26.73 E-value=22 Score=19.40 Aligned_cols=26 Identities=38% Similarity=1.003 Sum_probs=16.7
Q ss_pred eeeecCCCcceeccCCCchhh---HHHHhh
Q 037282 20 ACRVCGNPHAIIRKYGLMCCR---QCFRSN 46 (56)
Q Consensus 20 rC~~cGr~~g~irkfgl~~cR---~~fRe~ 46 (56)
.|.|||.+. .--.||...|. .-||..
T Consensus 2 ~C~VCg~~~-~~~~ygv~sC~~C~~FFrR~ 30 (70)
T PF00105_consen 2 KCKVCGDPA-SGYHYGVLSCNACKMFFRRS 30 (70)
T ss_dssp BSTTTSSBE-SEEETTEEEEHHHHHHHHHH
T ss_pred CCeECCCcc-Ccccccccccccceeeeeec
Confidence 489999864 33378886664 335553
No 24
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=26.67 E-value=39 Score=19.36 Aligned_cols=17 Identities=29% Similarity=0.589 Sum_probs=10.9
Q ss_pred CccceeeecCCCcceec
Q 037282 16 PGSRACRVCGNPHAIIR 32 (56)
Q Consensus 16 r~~~rC~~cGr~~g~ir 32 (56)
+.+-+|+.||+..-.++
T Consensus 14 ~tH~~CRRCGr~syhv~ 30 (61)
T COG2126 14 KTHIRCRRCGRRSYHVR 30 (61)
T ss_pred cceehhhhccchheeec
Confidence 66677888887543333
No 25
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=25.98 E-value=31 Score=21.74 Aligned_cols=30 Identities=23% Similarity=0.679 Sum_probs=18.6
Q ss_pred CCCccceeeecCCCcceeccCCCchhhHHHHhh
Q 037282 14 YGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSN 46 (56)
Q Consensus 14 ~~r~~~rC~~cGr~~g~irkfgl~~cR~~fRe~ 46 (56)
+|....+|.+||...|+-. -+.|..|.+.-
T Consensus 51 ~G~~~~rCIiCg~~~g~sd---AYYC~eC~~lE 80 (106)
T PF03660_consen 51 FGSLQGRCIICGSGPGVSD---AYYCWECVRLE 80 (106)
T ss_dssp TSSTTSB-TTTSSSB--EE----EE-HHHHHHT
T ss_pred CCCcCceEEEecCCCCccc---ceehhhhHhhh
Confidence 5788899999997777744 45588777653
No 26
>PRK08298 cytidine deaminase; Validated
Probab=25.65 E-value=33 Score=21.79 Aligned_cols=18 Identities=11% Similarity=0.397 Sum_probs=14.5
Q ss_pred eeccCCCchhhHHHHhhhhh
Q 037282 30 IIRKYGLMCCRQCFRSNAKE 49 (56)
Q Consensus 30 ~irkfgl~~cR~~fRe~A~~ 49 (56)
++.=-|. |||.+.|+..+
T Consensus 85 ~~sPCG~--CRQvl~Ef~~~ 102 (136)
T PRK08298 85 VLSPCGV--CQERLFYWGPD 102 (136)
T ss_pred ccCCChh--HHHHHHHhCCC
Confidence 5667788 99999999544
No 27
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=25.44 E-value=36 Score=19.49 Aligned_cols=20 Identities=35% Similarity=0.974 Sum_probs=12.9
Q ss_pred eeecCCCcceeccCCCchhhH
Q 037282 21 CRVCGNPHAIIRKYGLMCCRQ 41 (56)
Q Consensus 21 C~~cGr~~g~irkfgl~~cR~ 41 (56)
|.|||.+..- ..||...|+-
T Consensus 1 C~VCg~~~~g-~hyG~~sC~a 20 (81)
T cd07165 1 CKVCGDKASG-YHYGVTSCEG 20 (81)
T ss_pred CCccCccCcc-eEECchhhhh
Confidence 7788885422 3788766643
No 28
>KOG0808 consensus Carbon-nitrogen hydrolase [Amino acid transport and metabolism]
Probab=24.40 E-value=32 Score=25.48 Aligned_cols=14 Identities=36% Similarity=0.579 Sum_probs=12.2
Q ss_pred ceeccCCCchhhHH
Q 037282 29 AIIRKYGLMCCRQC 42 (56)
Q Consensus 29 g~irkfgl~~cR~~ 42 (56)
=+|.+.+||+|||+
T Consensus 339 llia~ldlnlcrq~ 352 (387)
T KOG0808|consen 339 LLIADLDLNLCRQY 352 (387)
T ss_pred eEEeecchHHHHHh
Confidence 46889999999997
No 29
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=24.23 E-value=20 Score=19.57 Aligned_cols=24 Identities=29% Similarity=0.653 Sum_probs=16.0
Q ss_pred cceeccCCCchhh---HHHHhhhhhcC
Q 037282 28 HAIIRKYGLMCCR---QCFRSNAKEIG 51 (56)
Q Consensus 28 ~g~irkfgl~~cR---~~fRe~A~~~G 51 (56)
..++++|||+.|- +-+.|.+.+.|
T Consensus 16 a~vf~~~gIDfCCgG~~~L~eA~~~~~ 42 (56)
T PF04405_consen 16 ARVFRKYGIDFCCGGNRSLEEACEEKG 42 (56)
T ss_pred HHHHHHcCCcccCCCCchHHHHHHHcC
Confidence 3688999999993 44555554433
No 30
>PTZ00334 trans-sialidase; Provisional
Probab=23.60 E-value=55 Score=26.62 Aligned_cols=34 Identities=18% Similarity=0.085 Sum_probs=22.0
Q ss_pred CCCccceeeecCCCc----c-eeccCCCchhhHHHHhhh
Q 037282 14 YGPGSRACRVCGNPH----A-IIRKYGLMCCRQCFRSNA 47 (56)
Q Consensus 14 ~~r~~~rC~~cGr~~----g-~irkfgl~~cR~~fRe~A 47 (56)
.-|-+||+++||..- | ==---..||+|+.|--..
T Consensus 10 APRTHNRRRVTGSSGRRREGrESEpQRPNMSRrvF~SAV 48 (780)
T PTZ00334 10 APRTHNRRRVTGSSGRRREGRESEPQRPNMSRRVFTSAV 48 (780)
T ss_pred CccccCcCcCCCCCCCcCCCCCCCCCCCCcchhhHHHHH
Confidence 356789999998631 1 111234788999997544
No 31
>PF13945 NST1: Salt tolerance down-regulator
Probab=22.82 E-value=19 Score=24.48 Aligned_cols=15 Identities=40% Similarity=0.813 Sum_probs=10.9
Q ss_pred ccceeeecCCCccee
Q 037282 17 GSRACRVCGNPHAII 31 (56)
Q Consensus 17 ~~~rC~~cGr~~g~i 31 (56)
..=.|.+|||.+-.|
T Consensus 140 h~C~C~vCgr~~~~i 154 (190)
T PF13945_consen 140 HSCSCSVCGRKRTAI 154 (190)
T ss_pred cCcccHHHhchhhHH
Confidence 345799999987443
No 32
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.04 E-value=55 Score=17.63 Aligned_cols=33 Identities=27% Similarity=0.412 Sum_probs=24.0
Q ss_pred CCCccceeeecCCC---cceeccCCCchhhHHHHhhhh
Q 037282 14 YGPGSRACRVCGNP---HAIIRKYGLMCCRQCFRSNAK 48 (56)
Q Consensus 14 ~~r~~~rC~~cGr~---~g~irkfgl~~cR~~fRe~A~ 48 (56)
..|+.+.|..||-. ||+.=|=.- |-+.|++.+.
T Consensus 7 TlRGirkCp~CGt~NG~R~~~CKN~~--C~~~~~~~~~ 42 (44)
T PF14952_consen 7 TLRGIRKCPKCGTYNGTRGLSCKNKS--CPQVFNVLDA 42 (44)
T ss_pred hHhccccCCcCcCccCcccccccCCc--cchhhhcccc
Confidence 46888999999985 555555555 7888887653
No 33
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.81 E-value=26 Score=21.45 Aligned_cols=26 Identities=31% Similarity=0.876 Sum_probs=17.8
Q ss_pred CccceeeecCCCcceec-cCCCchhhHH
Q 037282 16 PGSRACRVCGNPHAIIR-KYGLMCCRQC 42 (56)
Q Consensus 16 r~~~rC~~cGr~~g~ir-kfgl~~cR~~ 42 (56)
+....|..||+. .|-| ..||-.|+.|
T Consensus 33 ~~~~~Cp~C~~~-~VkR~a~GIW~C~kC 59 (89)
T COG1997 33 RAKHVCPFCGRT-TVKRIATGIWKCRKC 59 (89)
T ss_pred hcCCcCCCCCCc-ceeeeccCeEEcCCC
Confidence 345679999998 5555 5666667655
No 34
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.28 E-value=39 Score=18.01 Aligned_cols=11 Identities=55% Similarity=1.331 Sum_probs=8.7
Q ss_pred cceeeecCCCc
Q 037282 18 SRACRVCGNPH 28 (56)
Q Consensus 18 ~~rC~~cGr~~ 28 (56)
...|.+||||=
T Consensus 8 ~K~C~~C~rpf 18 (42)
T PF10013_consen 8 SKICPVCGRPF 18 (42)
T ss_pred CCcCcccCCcc
Confidence 46799999974
No 35
>PRK06848 hypothetical protein; Validated
Probab=20.98 E-value=49 Score=20.98 Aligned_cols=19 Identities=21% Similarity=0.485 Sum_probs=14.8
Q ss_pred ceeccCCCchhhHHHHhhhhh
Q 037282 29 AIIRKYGLMCCRQCFRSNAKE 49 (56)
Q Consensus 29 g~irkfgl~~cR~~fRe~A~~ 49 (56)
.++.=-|. |||.+.|+..+
T Consensus 92 ~~~~PCG~--CRQvl~E~~~~ 110 (139)
T PRK06848 92 WVVSPCGA--CRELISDYGKN 110 (139)
T ss_pred CccCCChh--hHHHHHHhCCC
Confidence 45667788 99999999654
No 36
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=20.76 E-value=46 Score=19.54 Aligned_cols=22 Identities=23% Similarity=0.770 Sum_probs=15.2
Q ss_pred ceeeecCCCcceeccCCCchhhH
Q 037282 19 RACRVCGNPHAIIRKYGLMCCRQ 41 (56)
Q Consensus 19 ~rC~~cGr~~g~irkfgl~~cR~ 41 (56)
..|.|||.+. .-..||...|.-
T Consensus 7 ~~C~VCg~~~-~g~hyGv~sC~a 28 (90)
T cd07168 7 KLCSICEDKA-TGLHYGIITCEG 28 (90)
T ss_pred CCCcccCCcC-cceEECceehhh
Confidence 3599999864 334888877743
No 37
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=20.73 E-value=48 Score=22.56 Aligned_cols=13 Identities=38% Similarity=0.567 Sum_probs=10.7
Q ss_pred hHHHHhhhhhcCc
Q 037282 40 RQCFRSNAKEIGF 52 (56)
Q Consensus 40 R~~fRe~A~~~Gf 52 (56)
=-.|||+|.++|.
T Consensus 32 G~iFR~~A~e~gm 44 (179)
T COG1102 32 GTIFREMARERGM 44 (179)
T ss_pred cHHHHHHHHHcCC
Confidence 3679999999874
No 38
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=20.55 E-value=71 Score=23.50 Aligned_cols=27 Identities=26% Similarity=0.614 Sum_probs=20.1
Q ss_pred CccceeeecCCCcceeccCCCchhhHHHHh
Q 037282 16 PGSRACRVCGNPHAIIRKYGLMCCRQCFRS 45 (56)
Q Consensus 16 r~~~rC~~cGr~~g~irkfgl~~cR~~fRe 45 (56)
.....|..||++-- -..=|| |..|+-|
T Consensus 4 ~~~~~C~~CGr~~~-~~~~~l--C~dC~~~ 30 (355)
T COG1499 4 ASTILCVRCGRSVD-PLIDGL--CGDCYVE 30 (355)
T ss_pred CcccEeccCCCcCc-hhhccc--cHHHHhc
Confidence 34568999999873 224467 9999988
No 39
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.52 E-value=56 Score=21.08 Aligned_cols=23 Identities=26% Similarity=0.798 Sum_probs=16.5
Q ss_pred eeecCCC-cce-----eccCCCchhhHHH
Q 037282 21 CRVCGNP-HAI-----IRKYGLMCCRQCF 43 (56)
Q Consensus 21 C~~cGr~-~g~-----irkfgl~~cR~~f 43 (56)
|.+||++ .|. |-.--|++|..|.
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~ 31 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR 31 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH
Confidence 9999975 333 4455678899887
No 40
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=20.10 E-value=34 Score=21.59 Aligned_cols=23 Identities=26% Similarity=0.496 Sum_probs=18.1
Q ss_pred CcceeccCCCchh--hHHHHhhhhh
Q 037282 27 PHAIIRKYGLMCC--RQCFRSNAKE 49 (56)
Q Consensus 27 ~~g~irkfgl~~c--R~~fRe~A~~ 49 (56)
|.-+-.+|||+++ |+.+|++..+
T Consensus 62 py~la~r~gI~~SvAr~vLR~Leee 86 (107)
T COG4901 62 PYVLASRYGINGSVARIVLRHLEEE 86 (107)
T ss_pred HHHHHHHhccchHHHHHHHHHHHhC
Confidence 3455678999887 9999999765
Done!