Query 039014
Match_columns 139
No_of_seqs 165 out of 288
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 05:28:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039014.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039014hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0187 40S ribosomal protein 100.0 4.9E-76 1.1E-80 449.5 7.8 128 1-128 1-128 (134)
2 PF00833 Ribosomal_S17e: Ribos 100.0 8.1E-70 1.8E-74 411.2 7.9 121 1-121 1-121 (121)
3 PTZ00154 40S ribosomal protein 100.0 6.7E-69 1.5E-73 411.8 9.4 127 1-128 1-128 (134)
4 COG1383 RPS17A Ribosomal prote 100.0 3.3E-36 7.2E-41 212.0 3.1 74 1-74 1-74 (74)
5 PRK01151 rps17E 30S ribosomal 100.0 1.2E-33 2.6E-38 191.1 3.5 58 2-59 1-58 (58)
6 PF08648 DUF1777: Protein of u 42.9 17 0.00038 28.0 1.9 18 97-114 121-138 (180)
7 COG0177 Nth Predicted EndoIII- 39.1 24 0.00051 29.3 2.2 26 3-28 83-108 (211)
8 PF08984 DUF1858: Domain of un 37.2 7.4 0.00016 25.3 -0.9 25 94-118 9-33 (59)
9 KOG1921 Endonuclease III [Repl 36.3 27 0.00058 30.6 2.1 24 5-28 135-158 (286)
10 PF05550 Peptidase_C53: Pestiv 34.9 17 0.00036 29.6 0.6 14 62-75 74-87 (168)
11 PRK13910 DNA glycosylase MutY; 28.0 50 0.0011 28.3 2.4 24 5-28 48-71 (289)
12 PF12596 Tnp_P_element_C: 87kD 27.8 22 0.00047 26.9 0.2 11 50-60 82-92 (106)
13 TIGR03252 uncharacterized HhH- 27.4 51 0.0011 26.8 2.3 56 3-58 78-139 (177)
14 PF02347 GDC-P: Glycine cleava 22.0 51 0.0011 30.0 1.4 20 99-118 8-27 (429)
15 PF04352 ProQ: ProQ/FINO famil 21.3 63 0.0014 23.8 1.6 61 7-67 4-76 (114)
No 1
>KOG0187 consensus 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-76 Score=449.47 Aligned_cols=128 Identities=66% Similarity=1.009 Sum_probs=126.3
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHHHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceeccchHHHhh
Q 039014 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERER 80 (139)
Q Consensus 1 MGrVRtk~VKr~a~~iiEkY~~~~t~DF~~NK~vv~eva~I~SKklRNkIAGYVThLmKriqrgpvrGisiklqEEerer 80 (139)
||+|||||||+|||+|+||||.++++||||||++|+|+|+||||+|||+||||+||||||||+|||||||||||||||||
T Consensus 1 MGrVrtktvKkaar~iiEkYy~rl~~dF~tNk~vceEvAII~SKkLrNkIAGyvtHLmkrIqkGpvRGISiKLQEEEREr 80 (134)
T KOG0187|consen 1 MGRVRTKTVKKAARVIIEKYYTRLTLDFHTNKRVCEEVAIIPSKKLRNKIAGYVTHLMKRIQKGPVRGISIKLQEEERER 80 (134)
T ss_pred CCcchhHHHHHHHHHHHHHHhccccccccccchhehheeeecchhhhhHHHHHHHHHHHHHHcCCccceeEeecHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCccccccCcceechHHHHHHHHcCCCCCCCceeecCCCCCCC
Q 039014 81 RMDFVPDESAIKTDEIKVDKETLDMLAALGMSDISGLVEVEPQSMITP 128 (139)
Q Consensus 81 rdnyvpe~S~ld~~~ieVD~~T~eMlk~l~~~~~~~~~v~~p~~~~~~ 128 (139)
|||||||+|+||+|+|+||+||+||||+|||++++|+++++|++++..
T Consensus 81 rdnyVPevSaLd~d~ieVD~dT~eMlk~lg~~~~~~~~~~~~~~~~~~ 128 (134)
T KOG0187|consen 81 RDNYVPEVSALDQDIIEVDPDTKEMLKLLGFGSLSGVQVTEPQVEMNF 128 (134)
T ss_pred hcccCcchhhcchhheeeChhHHHHHHHcCCCCcCceeeeccchhhcc
Confidence 999999999999999999999999999999999999999999988764
No 2
>PF00833 Ribosomal_S17e: Ribosomal S17; InterPro: IPR001210 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped in this family of ribosomal proteins, S17e. They include, vertebrate, Drosophila and Neurospora crassa (crp-3) S17's as well as yeast S17a (RP51A) and S17b (RP51B) and archaebacterial S17e [, , ].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1RQ6_A 2XZM_V 2XZN_V 3IZ6_Q 3IZB_Q 3O30_K 3O2Z_K 3U5G_R 3U5C_R.
Probab=100.00 E-value=8.1e-70 Score=411.24 Aligned_cols=121 Identities=63% Similarity=1.001 Sum_probs=111.7
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHHHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceeccchHHHhh
Q 039014 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERER 80 (139)
Q Consensus 1 MGrVRtk~VKr~a~~iiEkY~~~~t~DF~~NK~vv~eva~I~SKklRNkIAGYVThLmKriqrgpvrGisiklqEEerer 80 (139)
||+|||++||++|++|+|+||++||+|||+||++|+|+|+||||+|||+|||||||||||||+|||||||||||||||||
T Consensus 1 MG~Vrtk~IKr~a~~lieky~~~~t~DF~~NK~v~~eva~i~SKklRNkIAGYvThlmKriq~g~vrgis~klqEeErer 80 (121)
T PF00833_consen 1 MGRVRTKTIKRAARELIEKYYDRFTNDFETNKKVVEEVAIIPSKKLRNKIAGYVTHLMKRIQRGPVRGISIKLQEEERER 80 (121)
T ss_dssp ------HHHHHHHHHHHTTCTTTSSSSHHHHHHHHHHCSSSSSTTHHHHHHHHHHHHHHHHTSSSSTTCSSCCCCHHHHC
T ss_pred CCCCcchHHHHHHHHHHHHhhhHhhhhHHHHHHHHHHHccccchhhHHHHHHHHHHHHHHHHhccccccchhhhHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCccccccCcceechHHHHHHHHcCCCCCCCceeec
Q 039014 81 RMDFVPDESAIKTDEIKVDKETLDMLAALGMSDISGLVEVE 121 (139)
Q Consensus 81 rdnyvpe~S~ld~~~ieVD~~T~eMlk~l~~~~~~~~~v~~ 121 (139)
||||||++|++|++.|+|||||+||||+|||+++||++|+|
T Consensus 81 r~n~vpe~s~~d~~~i~VD~~T~emlk~l~~~~~~~~~~~~ 121 (121)
T PF00833_consen 81 RDNYVPEVSALDQEIIEVDPDTKEMLKSLGFGSLPNLQVTQ 121 (121)
T ss_dssp CTSSSSSSSEEESCS-ECTHHHHHHHHHTTTTSSS-EEEE-
T ss_pred hcccCCccccccCCcceeChhHHHHHHHcCCCCCCcceecC
Confidence 99999999999999999999999999999999999999986
No 3
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=100.00 E-value=6.7e-69 Score=411.76 Aligned_cols=127 Identities=68% Similarity=1.032 Sum_probs=123.6
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHHHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceeccchHHHhh
Q 039014 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERER 80 (139)
Q Consensus 1 MGrVRtk~VKr~a~~iiEkY~~~~t~DF~~NK~vv~eva~I~SKklRNkIAGYVThLmKriqrgpvrGisiklqEEerer 80 (139)
||+|||++||++|++|+|+||++||+|||+||++|+|+|+|+||+|||+||||||||||+||+|||||||||||||||||
T Consensus 1 MG~VRtk~VKr~a~~LiEkY~~~ft~DFe~NKkvv~eva~I~SKrlRNrIAGYIThlmkri~~gpvrgis~klqeeerer 80 (134)
T PTZ00154 1 MGRVRTKTVKRAARQIVEKYYSKLTLDFHTNKKIVEEVAIIPSKRLRNKIAGFVTHLMKRIQKGPVRGISLKLQEEERER 80 (134)
T ss_pred CCCcchHHHHHHHHHHHHHhHHHhcccHHHHHHHHHHHhcccchhhhhHHHHHHHHHHhhhccCCccccceehhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCccccccCcceechHHHHHHHHcCCCCCC-CceeecCCCCCCC
Q 039014 81 RMDFVPDESAIKTDEIKVDKETLDMLAALGMSDIS-GLVEVEPQSMITP 128 (139)
Q Consensus 81 rdnyvpe~S~ld~~~ieVD~~T~eMlk~l~~~~~~-~~~v~~p~~~~~~ 128 (139)
|||||||+|+||++.|+||+||+|||++|||+ +| ++++++|+.....
T Consensus 81 r~~yvPe~s~~~~~~i~vd~~t~~ml~~~~~~-~~~~~~~~~~~~~~~~ 128 (134)
T PTZ00154 81 RMDYVPEKSEVDIDNITVDQDTKDMLKSLGLG-VPRPVKVPDVARKKQK 128 (134)
T ss_pred hhccCCcchhcccceeEECHHHHHHHHHcCCC-CCCCceeccccccccc
Confidence 99999999999999999999999999999997 88 8999999876554
No 4
>COG1383 RPS17A Ribosomal protein S17E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-36 Score=211.98 Aligned_cols=74 Identities=55% Similarity=0.877 Sum_probs=73.0
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHHHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceeccc
Q 039014 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQ 74 (139)
Q Consensus 1 MGrVRtk~VKr~a~~iiEkY~~~~t~DF~~NK~vv~eva~I~SKklRNkIAGYVThLmKriqrgpvrGisiklq 74 (139)
||+|||++|||+|++|+|+|++.||.||++||++|+|+|.|+||+|||+|||||||||++++.|++++|++|+|
T Consensus 1 MG~IR~~~vKR~a~el~ekY~~~ft~dFe~NK~~V~e~~~i~SK~lRN~IAGYiT~~~~~~~~~~~~e~~~k~~ 74 (74)
T COG1383 1 MGRIRPKFVKRTARELIEKYPDKFTDDFETNKRLVEELANIQSKKLRNRIAGYITRLVKRIKEGPKREIEEKLQ 74 (74)
T ss_pred CCCcchHHHHHHHHHHHHHhHHHhcccHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHhhhcchhhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999876
No 5
>PRK01151 rps17E 30S ribosomal protein S17e; Validated
Probab=99.98 E-value=1.2e-33 Score=191.06 Aligned_cols=58 Identities=43% Similarity=0.744 Sum_probs=57.2
Q ss_pred CcccchhHHHHHHHHHHHhhcccCcchhHHHHHHHHhhccCcccccccccchhhhhhh
Q 039014 2 GRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMK 59 (139)
Q Consensus 2 GrVRtk~VKr~a~~iiEkY~~~~t~DF~~NK~vv~eva~I~SKklRNkIAGYVThLmK 59 (139)
|+|||++||++|++|+|+||++||+|||+||++|+|+|+|+||+|||+|||||||||+
T Consensus 1 G~Ir~k~IKr~a~~lieky~~~ft~DFe~NK~~v~e~a~i~SK~lRNrIAGYiT~~~~ 58 (58)
T PRK01151 1 GNIRPKYIKRTAEELLEKYPDLFTTDFETNKKLVEELTNIESKKVRNRIAGYITRKVK 58 (58)
T ss_pred CCcchHHHHHHHHHHHHHhHHHhcccHHHHHHHHHHHhcCccHhHHHHHhhhhhhccC
Confidence 8999999999999999999999999999999999999999999999999999999996
No 6
>PF08648 DUF1777: Protein of unknown function (DUF1777); InterPro: IPR013957 This entry shows eukaryotic proteins of unknown function. Some of the proteins are putative nucleic acid binding proteins.
Probab=42.91 E-value=17 Score=27.97 Aligned_cols=18 Identities=17% Similarity=0.431 Sum_probs=13.7
Q ss_pred eechHHHHHHHHcCCCCC
Q 039014 97 KVDKETLDMLAALGMSDI 114 (139)
Q Consensus 97 eVD~~T~eMlk~l~~~~~ 114 (139)
..++|-.+|++.|||+..
T Consensus 121 ~~~~de~~mmk~MGf~gF 138 (180)
T PF08648_consen 121 GEDDDEEEMMKMMGFGGF 138 (180)
T ss_pred ccchhHHHHHHhhccccc
Confidence 456677799999988643
No 7
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=39.15 E-value=24 Score=29.30 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=22.9
Q ss_pred cccchhHHHHHHHHHHHhhcccCcch
Q 039014 3 RVRTKTVKKSSRQVIERYYSRMTLDF 28 (139)
Q Consensus 3 rVRtk~VKr~a~~iiEkY~~~~t~DF 28 (139)
+.+.|+||.+|+.|+|+|.....+++
T Consensus 83 r~KAk~I~~~~~~l~e~~~g~vP~~~ 108 (211)
T COG0177 83 RNKAKNIKELARILLEKFGGEVPDTR 108 (211)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCchH
Confidence 45679999999999999999887777
No 8
>PF08984 DUF1858: Domain of unknown function (DUF1858); InterPro: IPR015077 This protein has no known function. It is found in various hypothetical bacterial proteins. ; PDB: 2K53_A 2K5E_A 2FI0_A.
Probab=37.21 E-value=7.4 Score=25.29 Aligned_cols=25 Identities=16% Similarity=0.321 Sum_probs=20.4
Q ss_pred CcceechHHHHHHHHcCCCCCCCce
Q 039014 94 DEIKVDKETLDMLAALGMSDISGLV 118 (139)
Q Consensus 94 ~~ieVD~~T~eMlk~l~~~~~~~~~ 118 (139)
|+++-.|++.+.|..+||.++.+..
T Consensus 9 el~~~yP~~~~il~~~gf~~l~~p~ 33 (59)
T PF08984_consen 9 ELLEQYPELIEILVSYGFHCLGNPV 33 (59)
T ss_dssp HHHHH-GGGHHHHHHTTGGGGGSCC
T ss_pred HHHHHCHHHHHHHHHcCCcccCCcH
Confidence 4577889999999999999887654
No 9
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=36.32 E-value=27 Score=30.58 Aligned_cols=24 Identities=13% Similarity=0.315 Sum_probs=19.2
Q ss_pred cchhHHHHHHHHHHHhhcccCcch
Q 039014 5 RTKTVKKSSRQVIERYYSRMTLDF 28 (139)
Q Consensus 5 Rtk~VKr~a~~iiEkY~~~~t~DF 28 (139)
+.+++|++|+-|.++|-.-+..+.
T Consensus 135 KA~ylkkta~IL~d~f~gDIP~~v 158 (286)
T KOG1921|consen 135 KAKYLKKTAKILQDKFDGDIPDTV 158 (286)
T ss_pred HHHHHHHHHHHHHHHhCCCCchhH
Confidence 458999999999999887665544
No 10
>PF05550 Peptidase_C53: Pestivirus Npro endopeptidase C53; InterPro: IPR008751 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C53 (clan C-). The active site residues occur in the order E, H, C in the sequence which is unlike that in any other family. They are unique to pestiviruses. The N-terminal cysteine peptidase (Npro) encoded by the bovine viral diarrhoea virus genome is responsible for the self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core [, , , ].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=34.93 E-value=17 Score=29.58 Aligned_cols=14 Identities=43% Similarity=0.767 Sum_probs=11.6
Q ss_pred hcCccccceeccch
Q 039014 62 QKGPVRGISLKLQE 75 (139)
Q Consensus 62 qrgpvrGisiklqE 75 (139)
.+|||.||+||..-
T Consensus 74 ~~GpVSGIYikpGP 87 (168)
T PF05550_consen 74 HRGPVSGIYIKPGP 87 (168)
T ss_pred cCCCcceEEecCCc
Confidence 36999999999753
No 11
>PRK13910 DNA glycosylase MutY; Provisional
Probab=28.04 E-value=50 Score=28.34 Aligned_cols=24 Identities=29% Similarity=0.455 Sum_probs=20.9
Q ss_pred cchhHHHHHHHHHHHhhcccCcch
Q 039014 5 RTKTVKKSSRQVIERYYSRMTLDF 28 (139)
Q Consensus 5 Rtk~VKr~a~~iiEkY~~~~t~DF 28 (139)
|.++++++|+.|+++|...|..++
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~ 71 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDY 71 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhH
Confidence 678999999999999988777765
No 12
>PF12596 Tnp_P_element_C: 87kDa Transposase; InterPro: IPR022242 This domain family is found in eukaryotes, and is typically between 78 and 110 amino acids in length. The family is found in association with PF05485 from PFAM. There are two completely conserved residues (D and G) that may be functionally important. This family is an 87kDa transposase protein which catalyses both the precise and imprecise excision of a nonautonomous P transposable element.
Probab=27.77 E-value=22 Score=26.87 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=9.1
Q ss_pred ccchhhhhhhh
Q 039014 50 IAGFSTHLMKR 60 (139)
Q Consensus 50 IAGYVThLmKr 60 (139)
|||||.|..|.
T Consensus 82 iaGyVa~k~~~ 92 (106)
T PF12596_consen 82 IAGYVAKKFRN 92 (106)
T ss_pred HHHHHHHHHHh
Confidence 89999997654
No 13
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=27.42 E-value=51 Score=26.75 Aligned_cols=56 Identities=16% Similarity=0.257 Sum_probs=37.5
Q ss_pred cccchhHHHHHHHHHHHhhcccCcch----hHHHHHHHHhhccC--cccccccccchhhhhh
Q 039014 3 RVRTKTVKKSSRQVIERYYSRMTLDF----HTNKKILEEVAIIP--SKRLRNKIAGFSTHLM 58 (139)
Q Consensus 3 rVRtk~VKr~a~~iiEkY~~~~t~DF----~~NK~vv~eva~I~--SKklRNkIAGYVThLm 58 (139)
+.+.++||.+|+.|+++|...+..=+ .....+.+++..+| -.+.-|-+.+|.-+..
T Consensus 78 ~~KAk~Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~ 139 (177)
T TIGR03252 78 GSMAKRVQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQL 139 (177)
T ss_pred HHHHHHHHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh
Confidence 36789999999999999998764332 23345567777776 3455566665544433
No 14
>PF02347 GDC-P: Glycine cleavage system P-protein; InterPro: IPR020580 This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T []. The reaction catalysed by this protein is: Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0055114 oxidation-reduction process; PDB: 1WYV_A 1WYT_C 1WYU_A.
Probab=22.00 E-value=51 Score=30.01 Aligned_cols=20 Identities=35% Similarity=0.644 Sum_probs=16.8
Q ss_pred chHHHHHHHHcCCCCCCCce
Q 039014 99 DKETLDMLAALGMSDISGLV 118 (139)
Q Consensus 99 D~~T~eMlk~l~~~~~~~~~ 118 (139)
|.|.++||+.+|+.|+.-|-
T Consensus 8 ~~~~~~ML~~iG~~sieeL~ 27 (429)
T PF02347_consen 8 DEDIQEMLDAIGVKSIEELF 27 (429)
T ss_dssp HHHHHHHHHHCT-SSTGGGG
T ss_pred HHHHHHHHHhcCCCCHHHHh
Confidence 56899999999999988776
No 15
>PF04352 ProQ: ProQ/FINO family; InterPro: IPR016103 This entry represents a structural domain consisting of six helices in an irregular non-globular array; it also contains two small beta-hairpins. This domain is found in the RNA-binding fertility inhibitor FinO that represses the conjugative transfer of F-like plasmids in Escherichia coli. FinO blocks the translation of TraJ, a positive activator of transcription of gene thereby protecting it from degradation, and catalyses FinP-TraJ mRNA hybridization. Interactions between these two RNAs are predicted to block the TraJ ribosomal binding site. FinO is largely helical, binds to its highest affinity binding site within FinP as a monomer, and contains two distinct RNA binding regions []. This entry also includes ProQ, which is required for full activation of the osmoprotectant transporter ProP in Escherichia coli [].; PDB: 3MW6_C 1DVO_A.
Probab=21.31 E-value=63 Score=23.81 Aligned_cols=61 Identities=16% Similarity=0.304 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHHHhhcccCcc--h-----hHHHHHHHHhhc---cCcccccccccchh--hhhhhhhhcCccc
Q 039014 7 KTVKKSSRQVIERYYSRMTLD--F-----HTNKKILEEVAI---IPSKRLRNKIAGFS--THLMKRIQKGPVR 67 (139)
Q Consensus 7 k~VKr~a~~iiEkY~~~~t~D--F-----~~NK~vv~eva~---I~SKklRNkIAGYV--ThLmKriqrgpvr 67 (139)
+.++.+-..|.++||.+|+.. | --.+.+.+.+.. +.-+.||.-++-|+ +++.+.+..|..|
T Consensus 4 ~~~~~~i~~L~~~fP~~F~~~~~~~PLkiGI~~dl~~~~~~~~~~s~~~lr~al~~y~~~~~Yl~a~~~g~~R 76 (114)
T PF04352_consen 4 KPIKELIARLQERFPEAFPKKGAPKPLKIGIFEDLAARLPEDGLLSKKELRRALRAYTRSPRYLKAVVEGAPR 76 (114)
T ss_dssp --HHHHHHHHTTT-GGGECTTE-C--B-TTHHHHHHHHHCCTT-S-HHHHHHHHHHHHCSHHHHHHHHCTSEE
T ss_pred hhHHHHHHHHHHHCHHhcCCCCCCCCchhhHHHHHHHHHHhcCCCCHHHHHHHHHHHHCCHHHHHHhcCCCce
Confidence 456777788899999999886 2 123566666665 56668888899888 5777788777554
Done!