Query 033129
Match_columns 126
No_of_seqs 120 out of 1012
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 10:10:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033129.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033129hhsearch_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 1.2E-45 2.6E-50 261.1 10.0 99 27-126 1-100 (100)
2 PRK08881 rpsN 30S ribosomal pr 100.0 2.8E-45 6.1E-50 259.5 9.8 100 27-126 1-101 (101)
3 CHL00074 rps14 ribosomal prote 100.0 2.3E-44 4.9E-49 254.5 9.6 99 27-126 1-100 (100)
4 KOG1741 Mitochondrial/chloropl 100.0 1.4E-40 3E-45 234.1 8.3 102 25-126 2-103 (103)
5 COG0199 RpsN Ribosomal protein 99.9 1.2E-27 2.7E-32 155.7 3.3 59 68-126 3-61 (61)
6 PF00253 Ribosomal_S14: Riboso 99.9 1.6E-26 3.5E-31 147.5 4.3 54 72-125 2-55 (55)
7 PRK08061 rpsN 30S ribosomal pr 99.9 3.1E-25 6.7E-30 144.5 4.7 58 67-126 4-61 (61)
8 PRK05766 rps14P 30S ribosomal 99.5 2.7E-15 5.8E-20 95.0 2.7 41 75-115 3-45 (52)
9 PTZ00218 40S ribosomal protein 98.3 3.9E-07 8.5E-12 58.1 1.7 32 84-115 14-47 (54)
10 KOG3506 40S ribosomal protein 91.5 0.072 1.6E-06 34.2 0.5 31 84-114 16-48 (56)
11 TIGR01764 excise DNA binding d 81.5 1.1 2.3E-05 25.6 1.6 26 98-123 7-32 (49)
12 PF12685 SpoIIIAH: SpoIIIAH-li 63.6 22 0.00048 27.3 5.5 45 26-77 87-131 (196)
13 PF12728 HTH_17: Helix-turn-he 62.3 5.9 0.00013 23.4 1.7 25 99-123 8-32 (51)
14 PF10346 Con-6: Conidiation pr 60.9 15 0.00032 21.6 3.1 26 51-76 9-34 (36)
15 cd04762 HTH_MerR-trunc Helix-T 58.7 8.1 0.00018 21.6 1.8 26 98-123 6-31 (49)
16 cd04761 HTH_MerR-SF Helix-Turn 45.1 18 0.0004 20.6 1.8 26 97-122 5-30 (49)
17 PRK04964 hypothetical protein; 37.3 50 0.0011 21.8 3.1 24 50-73 32-55 (66)
18 PF05930 Phage_AlpA: Prophage 35.5 8.7 0.00019 23.2 -0.7 25 95-119 6-30 (51)
19 PF07780 Spb1_C: Spb1 C-termin 34.4 2.4E+02 0.0052 22.6 7.9 71 34-104 120-197 (215)
20 PF06786 UPF0253: Uncharacteri 33.5 59 0.0013 21.4 2.9 24 50-73 32-55 (66)
21 smart00422 HTH_MERR helix_turn 28.7 49 0.0011 20.2 2.0 25 97-121 5-29 (70)
22 PF06353 DUF1062: Protein of u 26.9 33 0.00071 25.6 1.0 33 90-122 100-133 (142)
23 PF08880 QLQ: QLQ; InterPro: 25.3 1.5E+02 0.0032 17.2 4.4 26 42-67 8-33 (37)
24 PF13411 MerR_1: MerR HTH fami 24.6 61 0.0013 19.8 1.8 25 98-122 6-30 (69)
25 PF07340 Herpes_IE1: Cytomegal 22.3 5.4E+02 0.012 22.6 8.6 73 6-80 164-243 (392)
26 PF10654 DUF2481: Protein of u 21.0 1.9E+02 0.0041 21.3 4.0 37 43-80 7-43 (126)
No 1
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=100.00 E-value=1.2e-45 Score=261.05 Aligned_cols=99 Identities=33% Similarity=0.505 Sum_probs=95.7
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCCCCCCcccccccccccCCcchhhcccCcc
Q 033129 27 VSEK-RNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 105 (126)
Q Consensus 27 m~~~-~~~rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~LS 105 (126)
|+++ .+.||++++.++++||.+|.+||++++|+++|+++ ++|+.+|++||+||||||++|||++||||||||++||||
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 5655 56699999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 033129 106 RIVFRSLANQGMLMGVKKASW 126 (126)
Q Consensus 106 Ri~fR~la~~G~lpGv~KaSW 126 (126)
||+|||+|+.|+||||+||||
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=2.8e-45 Score=259.45 Aligned_cols=100 Identities=48% Similarity=0.705 Sum_probs=96.8
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCCCCCCcccccccccccCCcchhhcccCcc
Q 033129 27 VSEK-RNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 105 (126)
Q Consensus 27 m~~~-~~~rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~LS 105 (126)
|+++ .+.||.++++++++||.+|.+||++++|+++|.++|++|+.+|++||+|||+||++|||++||||||||++||||
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 5644 567999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 033129 106 RIVFRSLANQGMLMGVKKASW 126 (126)
Q Consensus 106 Ri~fR~la~~G~lpGv~KaSW 126 (126)
||+|||+|+.|+||||+||||
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=2.3e-44 Score=254.48 Aligned_cols=99 Identities=41% Similarity=0.639 Sum_probs=95.6
Q ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCCCCCCcccccccccccCCcchhhcccCcc
Q 033129 27 VSEK-RNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMS 105 (126)
Q Consensus 27 m~~~-~~~rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~LS 105 (126)
|+++ .+.||+++|.++++||.+|.+||++++|+++|.+ |++|+.+|++||+|||+||++|||++||||||||++||||
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 5644 5669999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCcccccC
Q 033129 106 RIVFRSLANQGMLMGVKKASW 126 (126)
Q Consensus 106 Ri~fR~la~~G~lpGv~KaSW 126 (126)
||+|||+|+.|+||||+||||
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=1.4e-40 Score=234.07 Aligned_cols=102 Identities=47% Similarity=0.792 Sum_probs=99.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCCCCCCcccccccccccCCcchhhcccCc
Q 033129 25 STVSEKRNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRM 104 (126)
Q Consensus 25 ~~m~~~~~~rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~L 104 (126)
+...++++.||.+||+++++||+.|..+|+|.+|++||.++|+++..+|++||+||.||+|+|||+.|||||||++.|+|
T Consensus 2 ~~~~~~r~~Rd~krRkl~~e~~~~R~slk~i~knp~LP~~~r~ea~~kl~alPrns~ptrI~NRCv~TGR~R~v~r~frL 81 (103)
T KOG1741|consen 2 TGAKKWRILRDVKRRKLFKEYELERRSLKEISKNPILPEKLRDEAAEKLQALPRNSAPTRIKNRCVFTGRPRGVYRDFRL 81 (103)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHhcCccccchHHHHHHHHhcCCcccccchhhh
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHhhhcCCCCCcccccC
Q 033129 105 SRIVFRSLANQGMLMGVKKASW 126 (126)
Q Consensus 105 SRi~fR~la~~G~lpGv~KaSW 126 (126)
|||+||++|+.|.||||+||||
T Consensus 82 sR~~FR~~A~~~~LpGv~rasW 103 (103)
T KOG1741|consen 82 SRHVFRELADAGALPGVTRASW 103 (103)
T ss_pred HHHHHHHHHHhccCcCcccccC
Confidence 9999999999999999999999
No 5
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.2e-27 Score=155.68 Aligned_cols=59 Identities=53% Similarity=0.750 Sum_probs=56.9
Q ss_pred HHHHHHhcCCCCCCcccccccccccCCcchhhcccCccHHHHHHhhhcCCCCCcccccC
Q 033129 68 KYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKASW 126 (126)
Q Consensus 68 ~a~~~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~LSRi~fR~la~~G~lpGv~KaSW 126 (126)
.++..|.++|+++++++++|||.+|||||||+|+|+|||++|||+|+.|+||||+||||
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 46677899999999999999999999999999999999999999999999999999999
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=99.93 E-value=1.6e-26 Score=147.48 Aligned_cols=54 Identities=65% Similarity=1.030 Sum_probs=52.2
Q ss_pred HHhcCCCCCCcccccccccccCCcchhhcccCccHHHHHHhhhcCCCCCccccc
Q 033129 72 KLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKAS 125 (126)
Q Consensus 72 ~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~LSRi~fR~la~~G~lpGv~KaS 125 (126)
+|+++|+++++++++|||++|||+|||+++|+|||++|||+|+.|+||||+|||
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=99.91 E-value=3.1e-25 Score=144.47 Aligned_cols=58 Identities=45% Similarity=0.748 Sum_probs=53.2
Q ss_pred HHHHHHHhcCCCCCCcccccccccccCCcchhhcccCccHHHHHHhhhcCCCCCcccccC
Q 033129 67 EKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKASW 126 (126)
Q Consensus 67 ~~a~~~L~~LPrnSs~tRirNRCv~TGR~Rgv~r~f~LSRi~fR~la~~G~lpGv~KaSW 126 (126)
+....+.++.|++ +||++|||++|||+|||+++|||||++|||+|+.|+||||+||||
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 4455667788875 599999999999999999999999999999999999999999999
No 8
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=99.54 E-value=2.7e-15 Score=95.01 Aligned_cols=41 Identities=22% Similarity=0.523 Sum_probs=39.4
Q ss_pred cCCCCCCcccccccccccCCcchhhcccC--ccHHHHHHhhhc
Q 033129 75 RLPRNSSFTRLRNRCIFTGRSRAVYEKFR--MSRIVFRSLANQ 115 (126)
Q Consensus 75 ~LPrnSs~tRirNRCv~TGR~Rgv~r~f~--LSRi~fR~la~~ 115 (126)
.+|+++++++++|||++|||++||+++|| |||++|||+|..
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=98.27 E-value=3.9e-07 Score=58.13 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=29.3
Q ss_pred cccccccccCCcchhhcccC--ccHHHHHHhhhc
Q 033129 84 RLRNRCIFTGRSRAVYEKFR--MSRIVFRSLANQ 115 (126)
Q Consensus 84 RirNRCv~TGR~Rgv~r~f~--LSRi~fR~la~~ 115 (126)
+-.++|.++||++|++|+|| +||..|||+|..
T Consensus 14 kGsr~C~vCg~~~gliRkygL~~CRqCFRe~A~~ 47 (54)
T PTZ00218 14 KGSRQCRVCSNRHGLIRKYGLNVCRQCFRENAEL 47 (54)
T ss_pred CCCCeeecCCCcchhhhhcCcchhhHHHHHhhHh
Confidence 44589999999999999999 999999999974
No 10
>KOG3506 consensus 40S ribosomal protein S29 [Translation, ribosomal structure and biogenesis]
Probab=91.49 E-value=0.072 Score=34.18 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=26.6
Q ss_pred cccccccccCCcchhhcccC--ccHHHHHHhhh
Q 033129 84 RLRNRCIFTGRSRAVYEKFR--MSRIVFRSLAN 114 (126)
Q Consensus 84 RirNRCv~TGR~Rgv~r~f~--LSRi~fR~la~ 114 (126)
+--.-|.+++.-.|.+++|| +||..||+.|.
T Consensus 16 ~GsrsC~vCsn~~gLIrKYGL~vcr~cfr~~a~ 48 (56)
T KOG3506|consen 16 QGSRSCRVCSNRHGLIRKYGLNVCRQCFREYAN 48 (56)
T ss_pred CCCcceeeeccchhHHHHhhhHHhHHHHHhhcc
Confidence 33567999999999999999 59999999875
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=81.52 E-value=1.1 Score=25.65 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=22.5
Q ss_pred hhcccCccHHHHHHhhhcCCCCCccc
Q 033129 98 VYEKFRMSRIVFRSLANQGMLMGVKK 123 (126)
Q Consensus 98 v~r~f~LSRi~fR~la~~G~lpGv~K 123 (126)
+-..+|+|+-.+++++..|.||+++.
T Consensus 7 ~a~~lgis~~ti~~~~~~g~i~~~~~ 32 (49)
T TIGR01764 7 AAEYLGVSKDTVYRLIHEGELPAYRV 32 (49)
T ss_pred HHHHHCCCHHHHHHHHHcCCCCeEEe
Confidence 45678999999999999999998753
No 12
>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=63.64 E-value=22 Score=27.27 Aligned_cols=45 Identities=20% Similarity=0.178 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCC
Q 033129 26 TVSEKRNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLP 77 (126)
Q Consensus 26 ~m~~~~~~rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LP 77 (126)
+++..++.||..|-+... .|+.|+.|++.+.+.+..|+.+|..|-
T Consensus 87 ~f~~~rl~Re~~r~~~~e-------~L~~ii~~~~~s~~~k~~A~~~~~~l~ 131 (196)
T PF12685_consen 87 YFAEARLEREQSRSKQIE-------TLKEIINNENASEEEKKEAQDKLLELT 131 (196)
T ss_dssp HHHHHHHHHHHHHHHHHH-------HHHHHHT-TTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH-------HHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 477888999988876655 688999999999999999998887653
No 13
>PF12728 HTH_17: Helix-turn-helix domain
Probab=62.27 E-value=5.9 Score=23.42 Aligned_cols=25 Identities=24% Similarity=0.171 Sum_probs=21.7
Q ss_pred hcccCccHHHHHHhhhcCCCCCccc
Q 033129 99 YEKFRMSRIVFRSLANQGMLMGVKK 123 (126)
Q Consensus 99 ~r~f~LSRi~fR~la~~G~lpGv~K 123 (126)
-..+|+|+-.+++++..|.||+++.
T Consensus 8 a~~l~is~~tv~~~~~~g~i~~~~~ 32 (51)
T PF12728_consen 8 AELLGISRSTVYRWIRQGKIPPFKI 32 (51)
T ss_pred HHHHCcCHHHHHHHHHcCCCCeEEe
Confidence 3567999999999999999999853
No 14
>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=60.95 E-value=15 Score=21.58 Aligned_cols=26 Identities=23% Similarity=0.323 Sum_probs=23.1
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHHhcC
Q 033129 51 LYKSLYRDVNLPTEVREKYLCKLARL 76 (126)
Q Consensus 51 ~LK~i~~n~~lp~~~r~~a~~~L~~L 76 (126)
=||+-+.|++.+.+-+..+...|..+
T Consensus 9 G~KAal~NPnvSeeaK~~A~~~Le~~ 34 (36)
T PF10346_consen 9 GYKAALHNPNVSEEAKQHAREKLEEM 34 (36)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHHHHc
Confidence 48999999999999999999888765
No 15
>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=58.69 E-value=8.1 Score=21.61 Aligned_cols=26 Identities=19% Similarity=0.310 Sum_probs=21.9
Q ss_pred hhcccCccHHHHHHhhhcCCCCCccc
Q 033129 98 VYEKFRMSRIVFRSLANQGMLMGVKK 123 (126)
Q Consensus 98 v~r~f~LSRi~fR~la~~G~lpGv~K 123 (126)
+-+.+|+|+.-++.+...|.+|..+.
T Consensus 6 ~a~~lgvs~~tl~~~~~~g~~~~~~~ 31 (49)
T cd04762 6 AAELLGVSPSTLRRWVKEGKLKAIRT 31 (49)
T ss_pred HHHHHCcCHHHHHHHHHcCCCCceeC
Confidence 44678999999999999999997653
No 16
>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=45.12 E-value=18 Score=20.61 Aligned_cols=26 Identities=15% Similarity=0.169 Sum_probs=21.7
Q ss_pred hhhcccCccHHHHHHhhhcCCCCCcc
Q 033129 97 AVYEKFRMSRIVFRSLANQGMLMGVK 122 (126)
Q Consensus 97 gv~r~f~LSRi~fR~la~~G~lpGv~ 122 (126)
-+-+.+|+|...+|.....|+||..+
T Consensus 5 e~a~~~gv~~~tlr~~~~~g~l~~~~ 30 (49)
T cd04761 5 ELAKLTGVSPSTLRYYERIGLLSPAR 30 (49)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCc
Confidence 34567899999999999999999544
No 17
>PRK04964 hypothetical protein; Provisional
Probab=37.31 E-value=50 Score=21.78 Aligned_cols=24 Identities=33% Similarity=0.371 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHH
Q 033129 50 KLYKSLYRDVNLPTEVREKYLCKL 73 (126)
Q Consensus 50 ~~LK~i~~n~~lp~~~r~~a~~~L 73 (126)
+.|..|..|..||.++|.+|...-
T Consensus 32 k~L~~IAad~~Lp~~vRe~AAfAA 55 (66)
T PRK04964 32 KALNEIAADEALPESVREKAAYAA 55 (66)
T ss_pred HHHHHHhccccCCHHHHHHHHHHH
Confidence 356678899999999998876543
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=35.51 E-value=8.7 Score=23.18 Aligned_cols=25 Identities=24% Similarity=0.268 Sum_probs=18.7
Q ss_pred cchhhcccCccHHHHHHhhhcCCCC
Q 033129 95 SRAVYEKFRMSRIVFRSLANQGMLM 119 (126)
Q Consensus 95 ~Rgv~r~f~LSRi~fR~la~~G~lp 119 (126)
...|...+|+||-.+..+...|.+|
T Consensus 6 ~~ev~~~~g~s~~ti~~~~k~g~FP 30 (51)
T PF05930_consen 6 IKEVAELLGVSRSTIYRLIKDGKFP 30 (51)
T ss_dssp HHHHHHHHSS-HHHHHHHHHHHH--
T ss_pred HHHHHHHHCCCHHHHHHHHhcccCC
Confidence 3457778899999999999999887
No 19
>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=34.44 E-value=2.4e+02 Score=22.55 Aligned_cols=71 Identities=20% Similarity=0.299 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH----hcCCCCCCccccccccc---ccCCcchhhcccCc
Q 033129 34 EDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKL----ARLPRNSSFTRLRNRCI---FTGRSRAVYEKFRM 104 (126)
Q Consensus 34 rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L----~~LPrnSs~tRirNRCv---~TGR~Rgv~r~f~L 104 (126)
+-.|++....+.|.-+.---.|..+..++.........+| ..-+...-.+-+..+=. .+|||+||-..|.+
T Consensus 120 kaRKK~Ra~kklek~kkKa~~I~~~~d~se~eK~~~i~kl~kka~~~~~kk~~~~VVakk~~~~~~~rp~Gvkg~~K~ 197 (215)
T PF07780_consen 120 KARKKRRAAKKLEKAKKKAEAIADDEDMSEREKAKQIKKLYKKAKKKKKKKKVKYVVAKKGNRGKKGRPKGVKGRYKM 197 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCcCCChHHHHHHHHHHHHHhhccCCCCCcEEEecCCCCCCCCCCCCCCCCCeee
Confidence 7888899999999999988889999999988876554444 22222221223333332 68999999888775
No 20
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=33.50 E-value=59 Score=21.43 Aligned_cols=24 Identities=29% Similarity=0.380 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHH
Q 033129 50 KLYKSLYRDVNLPTEVREKYLCKL 73 (126)
Q Consensus 50 ~~LK~i~~n~~lp~~~r~~a~~~L 73 (126)
+.|..|..|..||.++|.+|...-
T Consensus 32 k~Ln~iAad~~Lp~~vRE~AAfAA 55 (66)
T PF06786_consen 32 KTLNDIAADEALPEDVREQAAFAA 55 (66)
T ss_pred HHHHHHHcccccCHHHHHHHHHHH
Confidence 456778899999999998876543
No 21
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=28.66 E-value=49 Score=20.21 Aligned_cols=25 Identities=20% Similarity=0.098 Sum_probs=21.7
Q ss_pred hhhcccCccHHHHHHhhhcCCCCCc
Q 033129 97 AVYEKFRMSRIVFRSLANQGMLMGV 121 (126)
Q Consensus 97 gv~r~f~LSRi~fR~la~~G~lpGv 121 (126)
-+-+.+|+|...+|.....|++|..
T Consensus 5 eva~~~gvs~~tlr~~~~~gli~~~ 29 (70)
T smart00422 5 EVAKLAGVSVRTLRYYERIGLLPPP 29 (70)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCC
Confidence 4557789999999999999999876
No 22
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.86 E-value=33 Score=25.64 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=25.7
Q ss_pred cccCCcchhhc-ccCccHHHHHHhhhcCCCCCcc
Q 033129 90 IFTGRSRAVYE-KFRMSRIVFRSLANQGMLMGVK 122 (126)
Q Consensus 90 v~TGR~Rgv~r-~f~LSRi~fR~la~~G~lpGv~ 122 (126)
.++=|.=.+++ .+||||-.++.|...|.|.|..
T Consensus 100 ~~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 100 PFPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred CCCccHHHHHHHHhCcCHHHHHHHHHCCCEEecC
Confidence 34445555555 8999999999999999997653
No 23
>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=25.32 E-value=1.5e+02 Score=17.17 Aligned_cols=26 Identities=19% Similarity=0.368 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHH
Q 033129 42 ATKFELKRKLYKSLYRDVNLPTEVRE 67 (126)
Q Consensus 42 ~~k~e~~R~~LK~i~~n~~lp~~~r~ 67 (126)
....|..-.+||.+.+|..+|.++..
T Consensus 8 l~~L~~Qi~ayK~l~~~~pVP~~l~~ 33 (37)
T PF08880_consen 8 LQELRAQILAYKYLARNQPVPPQLQQ 33 (37)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence 45567777899999999999999763
No 24
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.56 E-value=61 Score=19.83 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=21.4
Q ss_pred hhcccCccHHHHHHhhhcCCCCCcc
Q 033129 98 VYEKFRMSRIVFRSLANQGMLMGVK 122 (126)
Q Consensus 98 v~r~f~LSRi~fR~la~~G~lpGv~ 122 (126)
+-+.+|+|...+|.....|++|-..
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 25
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=22.27 E-value=5.4e+02 Score=22.57 Aligned_cols=73 Identities=16% Similarity=0.141 Sum_probs=47.0
Q ss_pred hHHHHHhhhhhhhHHHHHhHH------HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCCC
Q 033129 6 SREKILSATSQCMNFWRKMST------VSEKRNI-EDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPR 78 (126)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~------m~~~~~~-rD~krR~l~~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LPr 78 (126)
..+.|+++.++.++..++++. +.|.... .|.++|-.|.-|...=...|.+.--.+.+.+. .|...|+.||.
T Consensus 164 ~~ekwm~clK~l~d~av~~s~kle~alk~Kv~~kkddL~~k~~Yt~~Ky~e~~mk~~~~PKttn~~s--QA~~fL~nlp~ 241 (392)
T PF07340_consen 164 KQEKWMACLKELADVAVNASKKLEKALKEKVQQKKDDLKRKCTYTCLKYIEMFMKNLCMPKTTNGQS--QAKAFLRNLPQ 241 (392)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHccCCCCCCcccHH--HHHHHHhcccc
Confidence 467889999999999888874 3344333 56666766666655555555444333333343 47777888987
Q ss_pred CC
Q 033129 79 NS 80 (126)
Q Consensus 79 nS 80 (126)
.+
T Consensus 242 ~d 243 (392)
T PF07340_consen 242 CD 243 (392)
T ss_pred CC
Confidence 65
No 26
>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=21.03 E-value=1.9e+02 Score=21.35 Aligned_cols=37 Identities=19% Similarity=0.228 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhcCCCCC
Q 033129 43 TKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNS 80 (126)
Q Consensus 43 ~k~e~~R~~LK~i~~n~~lp~~~r~~a~~~L~~LPrnS 80 (126)
+.-|-.|.++-.|+ |..||...+...+.+|+.|-...
T Consensus 7 ~NKerQreIIsyl~-n~dl~~~~~k~LqkeLn~Lm~~n 43 (126)
T PF10654_consen 7 ENKERQREIISYLV-NNDLSFSKRKELQKELNQLMNEN 43 (126)
T ss_pred hhHHHHHHHHHHHH-hCCCChHHHHHHHHHHHHHHhcc
Confidence 33455677777766 45689999999999998876543
Done!