Query 034126
Match_columns 103
No_of_seqs 113 out of 1019
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 10:03:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034126.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034126hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06911 rpsN 30S ribosomal pr 100.0 3.6E-47 7.9E-52 253.4 10.5 99 4-103 1-100 (100)
2 PRK08881 rpsN 30S ribosomal pr 100.0 3.6E-47 7.9E-52 253.9 10.3 100 4-103 1-101 (101)
3 CHL00074 rps14 ribosomal prote 100.0 5E-46 1.1E-50 248.0 10.1 99 4-103 1-100 (100)
4 KOG1741 Mitochondrial/chloropl 100.0 2.3E-42 5E-47 228.4 8.7 101 3-103 3-103 (103)
5 COG0199 RpsN Ribosomal protein 100.0 3.5E-29 7.5E-34 153.3 3.3 59 45-103 3-61 (61)
6 PF00253 Ribosomal_S14: Riboso 99.9 7E-28 1.5E-32 145.1 4.3 54 49-102 2-55 (55)
7 PRK08061 rpsN 30S ribosomal pr 99.9 9E-27 2E-31 142.7 4.7 58 44-103 4-61 (61)
8 PRK05766 rps14P 30S ribosomal 99.6 3.3E-16 7.1E-21 93.4 2.8 41 52-92 3-45 (52)
9 PTZ00218 40S ribosomal protein 98.6 2.2E-08 4.7E-13 60.0 1.7 38 53-92 8-47 (54)
10 KOG3506 40S ribosomal protein 95.6 0.0041 8.8E-08 37.4 0.5 31 61-91 16-48 (56)
11 TIGR01764 excise DNA binding d 86.0 0.57 1.2E-05 25.4 1.6 26 75-100 7-32 (49)
12 PF12728 HTH_17: Helix-turn-he 73.7 2.9 6.4E-05 23.4 1.9 25 76-100 8-32 (51)
13 PF10346 Con-6: Conidiation pr 68.0 10 0.00022 20.8 3.1 27 27-53 8-34 (36)
14 cd04762 HTH_MerR-trunc Helix-T 66.1 5.4 0.00012 21.2 1.8 26 75-100 6-31 (49)
15 cd04761 HTH_MerR-SF Helix-Turn 52.1 13 0.00028 20.1 1.8 25 75-99 6-30 (49)
16 PF12685 SpoIIIAH: SpoIIIAH-li 49.3 53 0.0011 23.7 5.1 42 5-53 89-130 (196)
17 PF10654 DUF2481: Protein of u 47.9 42 0.00092 23.2 4.1 37 20-57 7-43 (126)
18 PF05930 Phage_AlpA: Prophage 45.7 4.6 0.0001 23.0 -0.7 24 73-96 7-30 (51)
19 PRK04964 hypothetical protein; 44.5 37 0.00081 20.9 3.1 25 27-51 32-56 (66)
20 PF08880 QLQ: QLQ; InterPro: 40.0 64 0.0014 17.5 4.1 25 20-44 9-33 (37)
21 PF06786 UPF0253: Uncharacteri 40.0 46 0.00099 20.5 3.0 25 27-51 32-56 (66)
22 PF06353 DUF1062: Protein of u 38.4 17 0.00037 25.5 1.1 31 69-99 102-133 (142)
23 COG4840 Uncharacterized protei 35.9 89 0.0019 19.5 3.9 35 20-54 36-70 (71)
24 smart00422 HTH_MERR helix_turn 35.1 35 0.00076 19.7 2.0 25 74-98 5-29 (70)
25 PF04831 Popeye: Popeye protei 30.7 35 0.00075 24.5 1.6 19 74-92 8-26 (153)
26 PF07780 Spb1_C: Spb1 C-termin 29.5 2.5E+02 0.0053 21.2 7.5 72 10-81 119-197 (215)
27 COG4332 Uncharacterized protei 28.8 32 0.00069 25.6 1.2 24 76-99 146-169 (203)
28 PF13411 MerR_1: MerR HTH fami 28.8 48 0.001 19.2 1.8 25 75-99 6-30 (69)
29 PF10743 Phage_Cox: Regulatory 26.8 58 0.0012 21.2 2.0 21 79-99 22-42 (87)
30 cd04772 HTH_TioE_rpt1 First He 25.0 63 0.0014 20.7 2.0 26 75-100 6-31 (99)
31 COG4838 Uncharacterized protei 24.0 1.9E+02 0.0042 18.7 4.0 38 4-41 1-39 (92)
32 PF13976 gag_pre-integrs: GAG- 23.2 80 0.0017 18.2 2.1 24 77-100 29-53 (67)
33 PF00376 MerR: MerR family reg 20.7 70 0.0015 17.1 1.3 21 76-96 6-26 (38)
No 1
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=100.00 E-value=3.6e-47 Score=253.43 Aligned_cols=99 Identities=33% Similarity=0.505 Sum_probs=96.4
Q ss_pred hhhh-HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcCCCCCCccccccccccCCCcchhhcccCcc
Q 034126 4 VSEK-RNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 82 (103)
Q Consensus 4 m~~~-~~~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lS 82 (103)
||++ .++||++++.++++||.+|.+||+++.|+++|+++ ++++.+|++||+||||||++|||++||||||||++||||
T Consensus 1 Makks~i~rd~krr~l~~k~~~kR~~lK~i~~~~~l~~~~-~~a~~kL~~lPrnss~~R~rNRC~~TGR~Rgv~r~FgLs 79 (100)
T PRK06911 1 MAKKSMLMRESKRAKLVEKYRQRRNELKQLIKSSDDFQVI-MESQAKLAKLPVNSNPVRYVTRCKQCGRPHAVYRKFNLC 79 (100)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHH-HHHHHHHHhCCCccCcchhhcccCCCCCCcccccccCch
Confidence 7755 47899999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 034126 83 RIVFRSLANQGMLMGVKKASW 103 (103)
Q Consensus 83 R~~fR~~a~~G~lpGv~KssW 103 (103)
|+.|||+|+.|+||||+||||
T Consensus 80 Ri~~Rela~~G~lPGv~KaSW 100 (100)
T PRK06911 80 RICLRQQLMVGNIPGGRKSSW 100 (100)
T ss_pred HHHHHHHHHcCCCCCeecccC
Confidence 999999999999999999999
No 2
>PRK08881 rpsN 30S ribosomal protein S14; Reviewed
Probab=100.00 E-value=3.6e-47 Score=253.87 Aligned_cols=100 Identities=48% Similarity=0.705 Sum_probs=97.5
Q ss_pred hhhh-HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcCCCCCCccccccccccCCCcchhhcccCcc
Q 034126 4 VSEK-RNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 82 (103)
Q Consensus 4 m~~~-~~~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lS 82 (103)
||++ .++||.++|+++++||.+|.+||++++|+++|.++|++++.+|++||+|||+|+++|||++||||||||++||||
T Consensus 1 Makks~i~rd~krr~l~~k~~~kR~~lK~i~~~~~l~~~~r~~~~~kL~~lPr~ss~tRi~NRC~~TGR~Rgv~r~F~Ls 80 (101)
T PRK08881 1 MAKKSMIAREKKRKKLVAKYAAKRAELKAIISDPNLSDEERYEARLKLQKLPRNSSPTRLRNRCELTGRPRGYYRKFGLS 80 (101)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhCCcccchHHHhccccCCCCCCccccCcCch
Confidence 7754 578999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 034126 83 RIVFRSLANQGMLMGVKKASW 103 (103)
Q Consensus 83 R~~fR~~a~~G~lpGv~KssW 103 (103)
||+|||+|+.|+||||+||||
T Consensus 81 Ri~fRela~~G~lpGv~KsSW 101 (101)
T PRK08881 81 RIKLRELAHRGEIPGVVKASW 101 (101)
T ss_pred HHHHHHHHHcCCCCCeecccC
Confidence 999999999999999999999
No 3
>CHL00074 rps14 ribosomal protein S14
Probab=100.00 E-value=5e-46 Score=248.01 Aligned_cols=99 Identities=41% Similarity=0.639 Sum_probs=96.3
Q ss_pred hhhh-HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcCCCCCCccccccccccCCCcchhhcccCcc
Q 034126 4 VSEK-RNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 82 (103)
Q Consensus 4 m~~~-~~~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lS 82 (103)
||++ .+.||.++|.++++||.+|.+||+|+.|.++|.+ +++++.+|++||+|||+|+++|||++||||||||++||||
T Consensus 1 Mak~s~i~rd~krr~l~~k~~~kR~~lK~i~~~~~l~~~-r~~a~~kL~~lpr~ss~tRi~NRC~~TGR~Rgv~r~F~Ls 79 (100)
T CHL00074 1 MAKKSLIQREKKRQKLVQKYHLKRRSLKKEIKKVSSLSE-KWEIHGKLQSLPRNSAPTRLHNRCFLTGRPRGNYRDFGLS 79 (100)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcHH-HHHHHHHHHhCCcccchHHHhccccCCCCCCccccCcCch
Confidence 7754 5789999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 034126 83 RIVFRSLANQGMLMGVKKASW 103 (103)
Q Consensus 83 R~~fR~~a~~G~lpGv~KssW 103 (103)
|++|||+|+.|+||||+||||
T Consensus 80 Ri~~Re~a~~G~ipGv~KaSW 100 (100)
T CHL00074 80 RHVLREMAHACLLPGVTKSSW 100 (100)
T ss_pred HHHHHHHHHcCCCCCcccccC
Confidence 999999999999999999999
No 4
>KOG1741 consensus Mitochondrial/chloroplast ribosomal protein S14/S29 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-42 Score=228.37 Aligned_cols=101 Identities=48% Similarity=0.795 Sum_probs=98.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcCCCCCCccccccccccCCCcchhhcccCcc
Q 034126 3 TVSEKRNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 82 (103)
Q Consensus 3 ~m~~~~~~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lS 82 (103)
.-.++++.||.++|+++++||..|..+|+|.+|++||.+.|.++.++|+++|+||.||+|+|||+.|||+|||++.||||
T Consensus 3 ~~~~~r~~Rd~krRkl~~e~~~~R~slk~i~knp~LP~~~r~ea~~kl~alPrns~ptrI~NRCv~TGR~R~v~r~frLs 82 (103)
T KOG1741|consen 3 GAKKWRILRDVKRRKLFKEYELERRSLKEISKNPILPEKLRDEAAEKLQALPRNSAPTRIKNRCVFTGRPRGVYRDFRLS 82 (103)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHhcCccccchHHHHHHHHhcCCcccccchhhhH
Confidence 34577899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 034126 83 RIVFRSLANQGMLMGVKKASW 103 (103)
Q Consensus 83 R~~fR~~a~~G~lpGv~KssW 103 (103)
||.||++|+.|.||||+||||
T Consensus 83 R~~FR~~A~~~~LpGv~rasW 103 (103)
T KOG1741|consen 83 RHVFRELADAGALPGVTRASW 103 (103)
T ss_pred HHHHHHHHHhccCcCcccccC
Confidence 999999999999999999999
No 5
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.5e-29 Score=153.30 Aligned_cols=59 Identities=53% Similarity=0.750 Sum_probs=57.0
Q ss_pred HHHHHHhcCCCCCCccccccccccCCCcchhhcccCccHHHHHHhhhcCCCCCcccccC
Q 034126 45 KYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKASW 103 (103)
Q Consensus 45 ~~~~~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lSR~~fR~~a~~G~lpGv~KssW 103 (103)
.+...|.++|++++++++.|||.+|||||||+|+|+|||++|||+|+.|+||||+||||
T Consensus 3 ~a~~~~~~~p~~~~~~r~~nRC~~cGRprg~~Rkf~lcR~cfRE~A~~g~ipGv~K~sW 61 (61)
T COG0199 3 MAKLKLKALPRPKSPGRGRNRCRRCGRPRGVIRKFGLCRICFRELAHKGEIPGVKKASW 61 (61)
T ss_pred hhhhhhhcCCCCCccccccccccccCCCccchhhhhhHHHHHHHHhhccCCCCeEeccC
Confidence 46777899999999999999999999999999999999999999999999999999999
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=99.94 E-value=7e-28 Score=145.13 Aligned_cols=54 Identities=65% Similarity=1.030 Sum_probs=52.2
Q ss_pred HHhcCCCCCCccccccccccCCCcchhhcccCccHHHHHHhhhcCCCCCccccc
Q 034126 49 KLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKAS 102 (103)
Q Consensus 49 ~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lSR~~fR~~a~~G~lpGv~Kss 102 (103)
+|+++|+++++++++|||++|||+|||+++|+|||++|||+|+.|+||||+|||
T Consensus 2 kl~~~p~~s~~~r~~nrC~~tGR~rgv~r~f~lsR~~fR~~a~~g~l~G~~KsS 55 (55)
T PF00253_consen 2 KLSKLPRNSSPTRIKNRCVITGRSRGVIRKFGLSRICFRELASKGLLPGVKKSS 55 (55)
T ss_dssp HSTSSSSSSSCTGSCSSBSSSCSSSSBETTTSSBHHHHHHHHHTTSSTTEEES-
T ss_pred hhhhCCCCCCCCCCCeecccCCCceeeeccccccHHHHHHHHHcCCCCCEEeCC
Confidence 689999999999999999999999999999999999999999999999999997
No 7
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.93 E-value=9e-27 Score=142.74 Aligned_cols=58 Identities=45% Similarity=0.748 Sum_probs=53.5
Q ss_pred HHHHHHHhcCCCCCCccccccccccCCCcchhhcccCccHHHHHHhhhcCCCCCcccccC
Q 034126 44 EKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKASW 103 (103)
Q Consensus 44 ~~~~~~L~~lpr~ss~tri~nRC~~TGR~Rgv~r~f~lSR~~fR~~a~~G~lpGv~KssW 103 (103)
+....+.++.|++ +|+++|||++|||+|||+++|||||++|||+|+.|+||||+||||
T Consensus 4 ~~~~~k~~~~~k~--~~r~~nRC~~tGR~rgvir~fgl~R~~FRe~A~~G~ipGv~KasW 61 (61)
T PRK08061 4 KSLIAKAKRKPKF--KVRAYTRCERCGRPHSVYRKFGLCRICFRELAYKGQIPGVKKASW 61 (61)
T ss_pred hHHHHHhhcCCCC--CcccceeeecCCCCcceeccCCccHHHHHHHHHcCcCCCeeeccC
Confidence 4556677888885 699999999999999999999999999999999999999999999
No 8
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=99.61 E-value=3.3e-16 Score=93.36 Aligned_cols=41 Identities=22% Similarity=0.523 Sum_probs=39.3
Q ss_pred cCCCCCCccccccccccCCCcchhhcccC--ccHHHHHHhhhc
Q 034126 52 RLPRNSSFTRLRNRCIFTGRSRAVYEKFR--MSRIVFRSLANQ 92 (103)
Q Consensus 52 ~lpr~ss~tri~nRC~~TGR~Rgv~r~f~--lSR~~fR~~a~~ 92 (103)
.+|+++++++++|||++|||++||+++|| |||++|||+|..
T Consensus 3 ~~p~~~~~~r~~nrC~~~Gr~rgvirkf~l~lcR~~FRe~A~~ 45 (52)
T PRK05766 3 KPPKKRKYGKGARECQRCGRKQGLIRKYGLYLCRQCFREVAPK 45 (52)
T ss_pred CCCCCCCCCCCCceeecCCCCceeHHhhCCcccHHHHHHHHHH
Confidence 57999999999999999999999999999 999999999975
No 9
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=98.59 E-value=2.2e-08 Score=59.97 Aligned_cols=38 Identities=21% Similarity=0.383 Sum_probs=31.9
Q ss_pred CCCCCCccccccccccCCCcchhhcccC--ccHHHHHHhhhc
Q 034126 53 LPRNSSFTRLRNRCIFTGRSRAVYEKFR--MSRIVFRSLANQ 92 (103)
Q Consensus 53 lpr~ss~tri~nRC~~TGR~Rgv~r~f~--lSR~~fR~~a~~ 92 (103)
-|++-. +-.++|.++|+++|++|+|| |||++|||+|..
T Consensus 8 hpr~yG--kGsr~C~vCg~~~gliRkygL~~CRqCFRe~A~~ 47 (54)
T PTZ00218 8 HPRTYG--KGSRQCRVCSNRHGLIRKYGLNVCRQCFRENAEL 47 (54)
T ss_pred CCCcCC--CCCCeeecCCCcchhhhhcCcchhhHHHHHhhHh
Confidence 455433 44689999999999999999 999999999974
No 10
>KOG3506 consensus 40S ribosomal protein S29 [Translation, ribosomal structure and biogenesis]
Probab=95.63 E-value=0.0041 Score=37.36 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=27.1
Q ss_pred ccccccccCCCcchhhcccC--ccHHHHHHhhh
Q 034126 61 RLRNRCIFTGRSRAVYEKFR--MSRIVFRSLAN 91 (103)
Q Consensus 61 ri~nRC~~TGR~Rgv~r~f~--lSR~~fR~~a~ 91 (103)
+-..-|.+++..+|.+++|| +||.+||+.|.
T Consensus 16 ~GsrsC~vCsn~~gLIrKYGL~vcr~cfr~~a~ 48 (56)
T KOG3506|consen 16 QGSRSCRVCSNRHGLIRKYGLNVCRQCFREYAN 48 (56)
T ss_pred CCCcceeeeccchhHHHHhhhHHhHHHHHhhcc
Confidence 34567999999999999999 78999999875
No 11
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=85.98 E-value=0.57 Score=25.41 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=22.4
Q ss_pred hhcccCccHHHHHHhhhcCCCCCccc
Q 034126 75 VYEKFRMSRIVFRSLANQGMLMGVKK 100 (103)
Q Consensus 75 v~r~f~lSR~~fR~~a~~G~lpGv~K 100 (103)
+-..+|+|+-.+++++..|.||+++.
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i~~~~~ 32 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGELPAYRV 32 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCCCeEEe
Confidence 44678999999999999999998753
No 12
>PF12728 HTH_17: Helix-turn-helix domain
Probab=73.72 E-value=2.9 Score=23.36 Aligned_cols=25 Identities=24% Similarity=0.171 Sum_probs=21.7
Q ss_pred hcccCccHHHHHHhhhcCCCCCccc
Q 034126 76 YEKFRMSRIVFRSLANQGMLMGVKK 100 (103)
Q Consensus 76 ~r~f~lSR~~fR~~a~~G~lpGv~K 100 (103)
-..+|+|+-.+++++..|.||+++.
T Consensus 8 a~~l~is~~tv~~~~~~g~i~~~~~ 32 (51)
T PF12728_consen 8 AELLGISRSTVYRWIRQGKIPPFKI 32 (51)
T ss_pred HHHHCcCHHHHHHHHHcCCCCeEEe
Confidence 3467999999999999999999853
No 13
>PF10346 Con-6: Conidiation protein 6; InterPro: IPR018824 This entry represents a conserved region found in fungal conidiation-specific protein 6 []. This protein is expressed approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth [].
Probab=67.98 E-value=10 Score=20.80 Aligned_cols=27 Identities=22% Similarity=0.298 Sum_probs=23.5
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHhcC
Q 034126 27 KLYKSLYRDVNLPTEVREKYLCKLARL 53 (103)
Q Consensus 27 ~~lK~i~~n~~l~~~~r~~~~~~L~~l 53 (103)
.=||+-+.|+..+.+-+..+...|..+
T Consensus 8 ~G~KAal~NPnvSeeaK~~A~~~Le~~ 34 (36)
T PF10346_consen 8 GGYKAALHNPNVSEEAKQHAREKLEEM 34 (36)
T ss_pred HHHHHHhcCCCcCHHHHHHHHHHHHHc
Confidence 348899999999999999999888765
No 14
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=66.09 E-value=5.4 Score=21.15 Aligned_cols=26 Identities=19% Similarity=0.310 Sum_probs=21.7
Q ss_pred hhcccCccHHHHHHhhhcCCCCCccc
Q 034126 75 VYEKFRMSRIVFRSLANQGMLMGVKK 100 (103)
Q Consensus 75 v~r~f~lSR~~fR~~a~~G~lpGv~K 100 (103)
+-+.+|+|+..++.+...|.+|..+.
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~~~~~~ 31 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKLKAIRT 31 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCCCceeC
Confidence 44578999999999999999997643
No 15
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=52.07 E-value=13 Score=20.05 Aligned_cols=25 Identities=16% Similarity=0.175 Sum_probs=21.2
Q ss_pred hhcccCccHHHHHHhhhcCCCCCcc
Q 034126 75 VYEKFRMSRIVFRSLANQGMLMGVK 99 (103)
Q Consensus 75 v~r~f~lSR~~fR~~a~~G~lpGv~ 99 (103)
+-+.+|+|...+|.....|+||...
T Consensus 6 ~a~~~gv~~~tlr~~~~~g~l~~~~ 30 (49)
T cd04761 6 LAKLTGVSPSTLRYYERIGLLSPAR 30 (49)
T ss_pred HHHHHCcCHHHHHHHHHCCCCCCCc
Confidence 4567899999999999999999544
No 16
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=49.27 E-value=53 Score=23.72 Aligned_cols=42 Identities=21% Similarity=0.215 Sum_probs=29.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcC
Q 034126 5 SEKRNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARL 53 (103)
Q Consensus 5 ~~~~~~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~l 53 (103)
+..++.||..|-+.. ..|+.|+.|+..+.+.+-.|+.+|..|
T Consensus 89 ~~~rl~Re~~r~~~~-------e~L~~ii~~~~~s~~~k~~A~~~~~~l 130 (196)
T PF12685_consen 89 AEARLEREQSRSKQI-------ETLKEIINNENASEEEKKEAQDKLLEL 130 (196)
T ss_dssp HHHHHHHHHHHHHHH-------HHHHHHHT-TTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH-------HHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 445566666665543 468899999999999999998887655
No 17
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=47.91 E-value=42 Score=23.15 Aligned_cols=37 Identities=19% Similarity=0.250 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcCCCCC
Q 034126 20 TKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNS 57 (103)
Q Consensus 20 ~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~lpr~s 57 (103)
+.-|-.|.++-+|..+ .||...+.+.+.+|+.|-...
T Consensus 7 ~NKerQreIIsyl~n~-dl~~~~~k~LqkeLn~Lm~~n 43 (126)
T PF10654_consen 7 ENKERQREIISYLVNN-DLSFSKRKELQKELNQLMNEN 43 (126)
T ss_pred hhHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHHhcc
Confidence 4456678888888776 799999999999998776543
No 18
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=45.72 E-value=4.6 Score=22.98 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=18.1
Q ss_pred chhhcccCccHHHHHHhhhcCCCC
Q 034126 73 RAVYEKFRMSRIVFRSLANQGMLM 96 (103)
Q Consensus 73 Rgv~r~f~lSR~~fR~~a~~G~lp 96 (103)
..|...+|+||..+..+...|.+|
T Consensus 7 ~ev~~~~g~s~~ti~~~~k~g~FP 30 (51)
T PF05930_consen 7 KEVAELLGVSRSTIYRLIKDGKFP 30 (51)
T ss_dssp HHHHHHHSS-HHHHHHHHHHHH--
T ss_pred HHHHHHHCCCHHHHHHHHhcccCC
Confidence 456778899999999999999886
No 19
>PRK04964 hypothetical protein; Provisional
Probab=44.53 E-value=37 Score=20.92 Aligned_cols=25 Identities=36% Similarity=0.388 Sum_probs=19.8
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHh
Q 034126 27 KLYKSLYRDVNLPTEVREKYLCKLA 51 (103)
Q Consensus 27 ~~lK~i~~n~~l~~~~r~~~~~~L~ 51 (103)
+.|..|..|..||.+.|.++...-.
T Consensus 32 k~L~~IAad~~Lp~~vRe~AAfAAA 56 (66)
T PRK04964 32 KALNEIAADEALPESVREKAAYAAA 56 (66)
T ss_pred HHHHHHhccccCCHHHHHHHHHHHH
Confidence 5677788999999999988765443
No 20
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=40.00 E-value=64 Score=17.52 Aligned_cols=25 Identities=20% Similarity=0.398 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHH
Q 034126 20 TKFELKRKLYKSLYRDVNLPTEVRE 44 (103)
Q Consensus 20 ~k~e~~R~~lK~i~~n~~l~~~~r~ 44 (103)
...+..-.+||++.+|..+|.+...
T Consensus 9 ~~L~~Qi~ayK~l~~~~pVP~~l~~ 33 (37)
T PF08880_consen 9 QELRAQILAYKYLARNQPVPPQLQQ 33 (37)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHH
Confidence 4456667899999999999998854
No 21
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=39.96 E-value=46 Score=20.53 Aligned_cols=25 Identities=32% Similarity=0.397 Sum_probs=19.9
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHh
Q 034126 27 KLYKSLYRDVNLPTEVREKYLCKLA 51 (103)
Q Consensus 27 ~~lK~i~~n~~l~~~~r~~~~~~L~ 51 (103)
+.|..|..|..||.++|.++...-.
T Consensus 32 k~Ln~iAad~~Lp~~vRE~AAfAAA 56 (66)
T PF06786_consen 32 KTLNDIAADEALPEDVREQAAFAAA 56 (66)
T ss_pred HHHHHHHcccccCHHHHHHHHHHHH
Confidence 5677788999999999988765433
No 22
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=38.45 E-value=17 Score=25.55 Aligned_cols=31 Identities=19% Similarity=0.284 Sum_probs=24.2
Q ss_pred CCCcchhhc-ccCccHHHHHHhhhcCCCCCcc
Q 034126 69 TGRSRAVYE-KFRMSRIVFRSLANQGMLMGVK 99 (103)
Q Consensus 69 TGR~Rgv~r-~f~lSR~~fR~~a~~G~lpGv~ 99 (103)
+=|.-.+++ .+||||-.++.|...|.|.|..
T Consensus 102 ~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 102 PLRLDRLLARQLGLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred CccHHHHHHHHhCcCHHHHHHHHHCCCEEecC
Confidence 334445554 8999999999999999997753
No 23
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.88 E-value=89 Score=19.53 Aligned_cols=35 Identities=17% Similarity=0.265 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHhcCC
Q 034126 20 TKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLP 54 (103)
Q Consensus 20 ~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L~~lp 54 (103)
.+||..+-+|..+.+..++++.+-..+..+|..|.
T Consensus 36 ~~~edLtdiy~mvkkkenfSpsEmqaiA~eL~rlR 70 (71)
T COG4840 36 ANYEDLTDIYDMVKKKENFSPSEMQAIADELGRLR 70 (71)
T ss_pred ccHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Confidence 57899999999999888999988777777776653
No 24
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=35.15 E-value=35 Score=19.71 Aligned_cols=25 Identities=20% Similarity=0.098 Sum_probs=21.5
Q ss_pred hhhcccCccHHHHHHhhhcCCCCCc
Q 034126 74 AVYEKFRMSRIVFRSLANQGMLMGV 98 (103)
Q Consensus 74 gv~r~f~lSR~~fR~~a~~G~lpGv 98 (103)
-+-+.+|+|...+|.....|++|..
T Consensus 5 eva~~~gvs~~tlr~~~~~gli~~~ 29 (70)
T smart00422 5 EVAKLAGVSVRTLRYYERIGLLPPP 29 (70)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCC
Confidence 3556789999999999999999876
No 25
>PF04831 Popeye: Popeye protein conserved region; InterPro: IPR006916 The Popeye (POP) family of proteins, is restricted to vertebrates and is preferentially expressed in developing and adult striated muscle. It is represented by a conserved region which includes three potential transmembrane domains []. The strong conservation of POP genes during evolution and their preferential expression in heart and skeletal muscle suggest that these novel proteins may have an important function in these tissues in vertebrates.; GO: 0016020 membrane
Probab=30.69 E-value=35 Score=24.48 Aligned_cols=19 Identities=16% Similarity=0.511 Sum_probs=17.0
Q ss_pred hhhcccCccHHHHHHhhhc
Q 034126 74 AVYEKFRMSRIVFRSLANQ 92 (103)
Q Consensus 74 gv~r~f~lSR~~fR~~a~~ 92 (103)
.+|..+++||+.|++++++
T Consensus 8 ~lF~Pl~Vs~~~Fk~iv~~ 26 (153)
T PF04831_consen 8 TLFQPLKVSRQQFKKIVGC 26 (153)
T ss_pred HhccCcCCCHHHHHHHHhh
Confidence 4678899999999999988
No 26
>PF07780 Spb1_C: Spb1 C-terminal domain; InterPro: IPR012920 This presumed domain is found at the C terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis, for example P25582 from SWISSPROT []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005634 nucleus
Probab=29.54 E-value=2.5e+02 Score=21.16 Aligned_cols=72 Identities=19% Similarity=0.291 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHH----hcCCCCCCccccccccc---cCCCcchhhcccCc
Q 034126 10 IEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKL----ARLPRNSSFTRLRNRCI---FTGRSRAVYEKFRM 81 (103)
Q Consensus 10 ~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~~r~~~~~~L----~~lpr~ss~tri~nRC~---~TGR~Rgv~r~f~l 81 (103)
.+-.+++....+.|..+.---.|..+..++..+......+| ..-+..--.+-+..+=. .+|||.||-..|.+
T Consensus 119 AkaRKK~Ra~kklek~kkKa~~I~~~~d~se~eK~~~i~kl~kka~~~~~kk~~~~VVakk~~~~~~~rp~Gvkg~~K~ 197 (215)
T PF07780_consen 119 AKARKKRRAAKKLEKAKKKAEAIADDEDMSEREKAKQIKKLYKKAKKKKKKKKVKYVVAKKGNRGKKGRPKGVKGRYKM 197 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCcCCChHHHHHHHHHHHHHhhccCCCCCcEEEecCCCCCCCCCCCCCCCCCeee
Confidence 37778888889999888888889999999998876665554 22222111233333333 68999998877764
No 27
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.83 E-value=32 Score=25.61 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=21.4
Q ss_pred hcccCccHHHHHHhhhcCCCCCcc
Q 034126 76 YEKFRMSRIVFRSLANQGMLMGVK 99 (103)
Q Consensus 76 ~r~f~lSR~~fR~~a~~G~lpGv~ 99 (103)
-...||||-.|..++..|+|.|.+
T Consensus 146 ~seL~LSrS~lq~lie~g~Irgdt 169 (203)
T COG4332 146 ASELGLSRSELQRLIETGQIRGDT 169 (203)
T ss_pred HHHhCcCHHHHHHHHHcCceeecc
Confidence 347899999999999999999875
No 28
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.83 E-value=48 Score=19.16 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=21.2
Q ss_pred hhcccCccHHHHHHhhhcCCCCCcc
Q 034126 75 VYEKFRMSRIVFRSLANQGMLMGVK 99 (103)
Q Consensus 75 v~r~f~lSR~~fR~~a~~G~lpGv~ 99 (103)
+-+.+|+|...+|.....|+||-..
T Consensus 6 va~~~gvs~~tlr~y~~~gll~~~~ 30 (69)
T PF13411_consen 6 VAKLLGVSPSTLRYYEREGLLPPPR 30 (69)
T ss_dssp HHHHTTTTHHHHHHHHHTTSSTTBE
T ss_pred HHHHHCcCHHHHHHHHHhcCccccc
Confidence 4567899999999999999997654
No 29
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=26.82 E-value=58 Score=21.25 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=17.6
Q ss_pred cCccHHHHHHhhhcCCCCCcc
Q 034126 79 FRMSRIVFRSLANQGMLMGVK 99 (103)
Q Consensus 79 f~lSR~~fR~~a~~G~lpGv~ 99 (103)
-|-+--..|.|+..|+||.+.
T Consensus 22 IGKt~sAVr~Mi~~gKLP~i~ 42 (87)
T PF10743_consen 22 IGKTPSAVRKMIKAGKLPVIE 42 (87)
T ss_pred HCCCHHHHHHHHHcCCCCeEe
Confidence 356677899999999999875
No 30
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=25.02 E-value=63 Score=20.72 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=22.1
Q ss_pred hhcccCccHHHHHHhhhcCCCCCccc
Q 034126 75 VYEKFRMSRIVFRSLANQGMLMGVKK 100 (103)
Q Consensus 75 v~r~f~lSR~~fR~~a~~G~lpGv~K 100 (103)
+-+.+|+|...+|..-..|+||.+.+
T Consensus 6 ~A~~~gvs~~tlR~Ye~~Gll~~~~r 31 (99)
T cd04772 6 LARAIGLSPQTVRNYESLGLIPPAER 31 (99)
T ss_pred HHHHHCcCHHHHHHHHHcCCCCCCCc
Confidence 45678999999999999999987644
No 31
>COG4838 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.03 E-value=1.9e+02 Score=18.72 Aligned_cols=38 Identities=21% Similarity=0.212 Sum_probs=27.6
Q ss_pred hhhhHH-HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHH
Q 034126 4 VSEKRN-IEDHKRRLLATKFELKRKLYKSLYRDVNLPTE 41 (103)
Q Consensus 4 m~~~~~-~rd~krR~l~~k~e~~R~~lK~i~~n~~l~~~ 41 (103)
||+..+ -|+..-..+-..-|.....++.-..|.++|+-
T Consensus 1 Ma~~~idh~~~A~~lLk~DA~kIl~LIkVQldNLTlPqC 39 (92)
T COG4838 1 MAKEAIDHREKALELLKKDAEKILKLIKVQLDNLTLPQC 39 (92)
T ss_pred CchhhhhhHHHHHHHHHHhHHHHHHHHHHHhhcCCCCCC
Confidence 566666 46666666777777778888888888888863
No 32
>PF13976 gag_pre-integrs: GAG-pre-integrase domain
Probab=23.21 E-value=80 Score=18.17 Aligned_cols=24 Identities=29% Similarity=0.485 Sum_probs=19.9
Q ss_pred cccC-ccHHHHHHhhhcCCCCCccc
Q 034126 77 EKFR-MSRIVFRSLANQGMLMGVKK 100 (103)
Q Consensus 77 r~f~-lSR~~fR~~a~~G~lpGv~K 100 (103)
+.+| ++-..+..++..+.+||+..
T Consensus 29 ~RLGH~~~~~l~~l~~~~~~~~~~~ 53 (67)
T PF13976_consen 29 RRLGHPSFQVLKKLSKKGLLPGLKI 53 (67)
T ss_pred HhcCCCCHHHHHHHhhccCcCCCCC
Confidence 3455 88889999999999999864
No 33
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=20.73 E-value=70 Score=17.13 Aligned_cols=21 Identities=19% Similarity=0.259 Sum_probs=16.9
Q ss_pred hcccCccHHHHHHhhhcCCCC
Q 034126 76 YEKFRMSRIVFRSLANQGMLM 96 (103)
Q Consensus 76 ~r~f~lSR~~fR~~a~~G~lp 96 (103)
-+.+|+|-..+|.....|+||
T Consensus 6 A~~~gvs~~tlR~ye~~Gll~ 26 (38)
T PF00376_consen 6 AKLLGVSPRTLRYYEREGLLP 26 (38)
T ss_dssp HHHHTS-HHHHHHHHHTTSS-
T ss_pred HHHHCCCHHHHHHHHHCCCCC
Confidence 356899999999999999995
Done!