Query 032415
Match_columns 141
No_of_seqs 168 out of 292
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 13:48:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032415.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032415hhsearch_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 3.9E-75 8.5E-80 445.5 8.0 126 1-126 1-126 (134)
2 PTZ00154 40S ribosomal protein 100.0 4.7E-69 1E-73 413.5 9.8 127 1-128 1-128 (134)
3 PF00833 Ribosomal_S17e: Ribos 100.0 2.7E-69 5.9E-74 409.3 8.1 121 1-121 1-121 (121)
4 COG1383 RPS17A Ribosomal prote 100.0 4.3E-36 9.4E-41 211.9 3.2 74 1-74 1-74 (74)
5 PRK01151 rps17E 30S ribosomal 100.0 1.4E-33 3E-38 191.2 3.4 58 2-59 1-58 (58)
6 PF08648 DUF1777: Protein of u 46.5 15 0.00032 28.4 2.0 18 97-114 121-138 (180)
7 COG0177 Nth Predicted EndoIII- 38.1 25 0.00055 29.2 2.2 26 3-28 83-108 (211)
8 PF08984 DUF1858: Domain of un 31.3 11 0.00023 24.6 -0.8 25 94-118 9-33 (59)
9 PF05550 Peptidase_C53: Pestiv 30.4 22 0.00047 29.0 0.6 13 62-74 74-86 (168)
10 PRK13910 DNA glycosylase MutY; 27.8 50 0.0011 28.4 2.4 24 5-28 48-71 (289)
11 PF12596 Tnp_P_element_C: 87kD 27.2 23 0.00051 26.8 0.3 10 50-59 82-91 (106)
12 TIGR03252 uncharacterized HhH- 25.7 58 0.0012 26.5 2.3 57 3-59 78-140 (177)
13 PF02347 GDC-P: Glycine cleava 24.8 40 0.00086 30.8 1.3 24 99-122 8-32 (429)
14 COG5175 MOT2 Transcriptional r 24.0 1.3E+02 0.0028 27.9 4.3 64 58-124 381-450 (480)
15 PF04352 ProQ: ProQ/FINO famil 22.2 64 0.0014 23.9 1.8 61 7-67 4-76 (114)
16 PF11380 DUF3184: Protein of u 20.7 65 0.0014 31.4 1.9 38 18-57 400-438 (691)
17 COG2012 RPB5 DNA-directed RNA 20.6 71 0.0015 23.3 1.7 36 83-124 13-50 (80)
No 1
>KOG0187 consensus 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.9e-75 Score=445.51 Aligned_cols=126 Identities=66% Similarity=1.018 Sum_probs=125.0
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHhHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceecccHHHHhh
Q 032415 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERER 80 (141)
Q Consensus 1 MGrVRtk~VKr~ar~liEkY~~~~t~DFe~NK~vv~eva~I~SKrlRNkIAGYVThLmKriqrgpvrgisiklqEEerer 80 (141)
||+|||||||++|++|+||||.++++||||||++|+|+|+|+||+|||+||||+||||||||+|||||||||||||||||
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 ccCCCCCcccccccceeechHHHHHHHHcCCCCCCCeeeeCCCCCC
Q 032415 81 RMDFVPDESAIKTDQIEVDKETLDMLEALGMNEIPGLVRVDPVAPG 126 (141)
Q Consensus 81 r~nyvpe~S~ld~~~i~VD~~T~eMlk~l~~~~~~~~~~~~~~~~~ 126 (141)
|||||||+|+||+|+|+||+||+||||+|||++++|+++++|++++
T Consensus 81 rdnyVPevSaLd~d~ieVD~dT~eMlk~lg~~~~~~~~~~~~~~~~ 126 (134)
T KOG0187|consen 81 RDNYVPEVSALDQDIIEVDPDTKEMLKLLGFGSLSGVQVTEPQVEM 126 (134)
T ss_pred hcccCcchhhcchhheeeChhHHHHHHHcCCCCcCceeeeccchhh
Confidence 9999999999999999999999999999999999999999999886
No 2
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=100.00 E-value=4.7e-69 Score=413.54 Aligned_cols=127 Identities=69% Similarity=1.064 Sum_probs=123.2
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHhHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceecccHHHHhh
Q 032415 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERER 80 (141)
Q Consensus 1 MGrVRtk~VKr~ar~liEkY~~~~t~DFe~NK~vv~eva~I~SKrlRNkIAGYVThLmKriqrgpvrgisiklqEEerer 80 (141)
||+|||++||++|++|+|+||++||+|||+||++|+|+|+|+||+|||+||||||||||+||+|||||||||||||||||
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 ccCCCCCcccccccceeechHHHHHHHHcCCCCCC-CeeeeCCCCCCCC
Q 032415 81 RMDFVPDESAIKTDQIEVDKETLDMLEALGMNEIP-GLVRVDPVAPGVE 128 (141)
Q Consensus 81 r~nyvpe~S~ld~~~i~VD~~T~eMlk~l~~~~~~-~~~~~~~~~~~~~ 128 (141)
|||||||+|+||++.|+||+||+|||++|||+ +| ++++++|+.....
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 8999999765443
No 3
>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=2.7e-69 Score=409.27 Aligned_cols=121 Identities=64% Similarity=1.030 Sum_probs=111.6
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHhHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceecccHHHHhh
Q 032415 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERER 80 (141)
Q Consensus 1 MGrVRtk~VKr~ar~liEkY~~~~t~DFe~NK~vv~eva~I~SKrlRNkIAGYVThLmKriqrgpvrgisiklqEEerer 80 (141)
||+|||++||++|++|+|+||++||+|||+||++|+|+|+|+||+|||+||||||||||+||+|||||||||||||||||
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 ccCCCCCcccccccceeechHHHHHHHHcCCCCCCCeeeeC
Q 032415 81 RMDFVPDESAIKTDQIEVDKETLDMLEALGMNEIPGLVRVD 121 (141)
Q Consensus 81 r~nyvpe~S~ld~~~i~VD~~T~eMlk~l~~~~~~~~~~~~ 121 (141)
||||||++|+||++.|+|||||+||||+|||+++||++|+|
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 4
>COG1383 RPS17A Ribosomal protein S17E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-36 Score=211.87 Aligned_cols=74 Identities=55% Similarity=0.877 Sum_probs=73.0
Q ss_pred CCcccchhHHHHHHHHHHHhhcccCcchhHhHHHHHHhhccCcccccccccchhhhhhhhhhcCccccceeccc
Q 032415 1 MGRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQ 74 (141)
Q Consensus 1 MGrVRtk~VKr~ar~liEkY~~~~t~DFe~NK~vv~eva~I~SKrlRNkIAGYVThLmKriqrgpvrgisiklq 74 (141)
||+|||++|||+|++|+|+||+.||+||++||++|+|++.|+||+|||+|||||||||++++.|++++|++|+|
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=1.4e-33 Score=191.18 Aligned_cols=58 Identities=43% Similarity=0.744 Sum_probs=57.2
Q ss_pred CcccchhHHHHHHHHHHHhhcccCcchhHhHHHHHHhhccCcccccccccchhhhhhh
Q 032415 2 GRVRTKTVKKSSRQVIERYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMK 59 (141)
Q Consensus 2 GrVRtk~VKr~ar~liEkY~~~~t~DFe~NK~vv~eva~I~SKrlRNkIAGYVThLmK 59 (141)
|+|||++||++|++|+|+||++||+|||+||++|+|+|+|+||+|||+|||||||||+
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=46.50 E-value=15 Score=28.41 Aligned_cols=18 Identities=17% Similarity=0.449 Sum_probs=13.9
Q ss_pred eechHHHHHHHHcCCCCC
Q 032415 97 EVDKETLDMLEALGMNEI 114 (141)
Q Consensus 97 ~VD~~T~eMlk~l~~~~~ 114 (141)
..++|-.+|++.|||+..
T Consensus 121 ~~~~de~~mmk~MGf~gF 138 (180)
T PF08648_consen 121 GEDDDEEEMMKMMGFGGF 138 (180)
T ss_pred ccchhHHHHHHhhccccc
Confidence 457777799999998743
No 7
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=38.15 E-value=25 Score=29.21 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=22.8
Q ss_pred cccchhHHHHHHHHHHHhhcccCcch
Q 032415 3 RVRTKTVKKSSRQVIERYYSRMTLDF 28 (141)
Q Consensus 3 rVRtk~VKr~ar~liEkY~~~~t~DF 28 (141)
+.+.|+||.+|+.|+|+|.....+++
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=31.33 E-value=11 Score=24.60 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=19.9
Q ss_pred cceeechHHHHHHHHcCCCCCCCee
Q 032415 94 DQIEVDKETLDMLEALGMNEIPGLV 118 (141)
Q Consensus 94 ~~i~VD~~T~eMlk~l~~~~~~~~~ 118 (141)
|+++-.|++.+.|..+||.++.+-.
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 4677889999999999999876643
No 9
>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=30.37 E-value=22 Score=29.02 Aligned_cols=13 Identities=46% Similarity=0.838 Sum_probs=11.2
Q ss_pred hcCccccceeccc
Q 032415 62 QKGPVRGISLKLQ 74 (141)
Q Consensus 62 qrgpvrgisiklq 74 (141)
.+|||.||+||.-
T Consensus 74 ~~GpVSGIYikpG 86 (168)
T PF05550_consen 74 HRGPVSGIYIKPG 86 (168)
T ss_pred cCCCcceEEecCC
Confidence 4799999999975
No 10
>PRK13910 DNA glycosylase MutY; Provisional
Probab=27.77 E-value=50 Score=28.36 Aligned_cols=24 Identities=29% Similarity=0.455 Sum_probs=21.0
Q ss_pred cchhHHHHHHHHHHHhhcccCcch
Q 032415 5 RTKTVKKSSRQVIERYYSRMTLDF 28 (141)
Q Consensus 5 Rtk~VKr~ar~liEkY~~~~t~DF 28 (141)
|.++++++|+.|+++|...|..++
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~ 71 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDY 71 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhH
Confidence 678999999999999988777765
No 11
>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=27.21 E-value=23 Score=26.77 Aligned_cols=10 Identities=30% Similarity=0.684 Sum_probs=8.8
Q ss_pred ccchhhhhhh
Q 032415 50 IAGFSTHLMK 59 (141)
Q Consensus 50 IAGYVThLmK 59 (141)
|||||.|..|
T Consensus 82 iaGyVa~k~~ 91 (106)
T PF12596_consen 82 IAGYVAKKFR 91 (106)
T ss_pred HHHHHHHHHH
Confidence 8999999776
No 12
>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=25.65 E-value=58 Score=26.50 Aligned_cols=57 Identities=16% Similarity=0.251 Sum_probs=37.3
Q ss_pred cccchhHHHHHHHHHHHhhcccCcchh----HhHHHHHHhhccC--cccccccccchhhhhhh
Q 032415 3 RVRTKTVKKSSRQVIERYYSRMTLDFH----TNKKILEEVAIIP--SKRLRNKIAGFSTHLMK 59 (141)
Q Consensus 3 rVRtk~VKr~ar~liEkY~~~~t~DFe----~NK~vv~eva~I~--SKrlRNkIAGYVThLmK 59 (141)
+.+.++||.+|+.|+++|...+..=+. ....+.+++..+| -.+.-|-+.+|.-+..+
T Consensus 78 ~~KAk~Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~~ 140 (177)
T TIGR03252 78 GSMAKRVQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQLG 140 (177)
T ss_pred HHHHHHHHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHhC
Confidence 467899999999999999987643222 2345566777675 34556666665544333
No 13
>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=24.84 E-value=40 Score=30.76 Aligned_cols=24 Identities=33% Similarity=0.584 Sum_probs=18.2
Q ss_pred chHHHHHHHHcCCCCCCCee-eeCC
Q 032415 99 DKETLDMLEALGMNEIPGLV-RVDP 122 (141)
Q Consensus 99 D~~T~eMlk~l~~~~~~~~~-~~~~ 122 (141)
|.|.++||+.+|+.|+.-|- -.-|
T Consensus 8 ~~~~~~ML~~iG~~sieeL~~~~IP 32 (429)
T PF02347_consen 8 DEDIQEMLDAIGVKSIEELFDSDIP 32 (429)
T ss_dssp HHHHHHHHHHCT-SSTGGGG-TTS-
T ss_pred HHHHHHHHHhcCCCCHHHHhhhhCC
Confidence 57899999999999998776 4444
No 14
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=24.02 E-value=1.3e+02 Score=27.93 Aligned_cols=64 Identities=17% Similarity=0.215 Sum_probs=44.6
Q ss_pred hhhhhcCccccceecccHHHHhhccCC-----CCCcc-cccccceeechHHHHHHHHcCCCCCCCeeeeCCCC
Q 032415 58 MKRIQKGPVRGISLKLQEEERERRMDF-----VPDES-AIKTDQIEVDKETLDMLEALGMNEIPGLVRVDPVA 124 (141)
Q Consensus 58 mKriqrgpvrgisiklqEEererr~ny-----vpe~S-~ld~~~i~VD~~T~eMlk~l~~~~~~~~~~~~~~~ 124 (141)
+-.+|+ |-||||-.||--...|+- +-..+ .|-.+.|+.|...-+||.++++|-..+..+++-++
T Consensus 381 l~~~qk---r~~~i~sdee~~~kw~~ks~n~l~~~l~~i~a~~~~d~~~~~vq~lq~~~~~v~~~~ti~d~~~ 450 (480)
T COG5175 381 LSNYQK---RPISIKSDEETYKKWDKKSDNTLANKLVEILAIKPIDYTASVVQFLQSVNVGVNDNITITDNTK 450 (480)
T ss_pred chhhhc---CCccCCchHHHHHHHhhhhhHHHHHHHHHHHccCCccccHHHHHHHHhcccccccceeeecCcc
Confidence 345777 678999977766665541 11111 12457889999999999999999777888876543
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=22.19 E-value=64 Score=23.86 Aligned_cols=61 Identities=16% Similarity=0.297 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHHhhcccCcch-------hHhHHHHHHhhc---cCcccccccccchh--hhhhhhhhcCccc
Q 032415 7 KTVKKSSRQVIERYYSRMTLDF-------HTNKKILEEVAI---IPSKRLRNKIAGFS--THLMKRIQKGPVR 67 (141)
Q Consensus 7 k~VKr~ar~liEkY~~~~t~DF-------e~NK~vv~eva~---I~SKrlRNkIAGYV--ThLmKriqrgpvr 67 (141)
+.++.+-..|.++||.+|+..- --.+.+.+.+.. +.-+.||.-++-|+ +++.+.+..|..|
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 4567777889999999998862 123566666665 66678888899998 5777777777544
No 16
>PF11380 DUF3184: Protein of unknown function (DUF3184); InterPro: IPR021520 This eukaryotic family of proteins has no known function. ; GO: 0016772 transferase activity, transferring phosphorus-containing groups
Probab=20.66 E-value=65 Score=31.38 Aligned_cols=38 Identities=34% Similarity=0.478 Sum_probs=28.2
Q ss_pred HHhhcccCcchhHhHHHHHHhhccCcccc-cccccchhhhh
Q 032415 18 ERYYSRMTLDFHTNKKILEEVAIIPSKRL-RNKIAGFSTHL 57 (141)
Q Consensus 18 EkY~~~~t~DFe~NK~vv~eva~I~SKrl-RNkIAGYVThL 57 (141)
|--|.+|++|+..|+++.+++.. ++.| -|-=|||-|--
T Consensus 400 e~~y~kf~dd~~~N~~~m~rv~q--~~plffNINagfs~~e 438 (691)
T PF11380_consen 400 ECMYGKFVDDLTANKRVMERVRQ--TNPLFFNINAGFSSAE 438 (691)
T ss_pred hhhhhhhccchhHHHHHHHHHHh--cCCceEEeccccCchH
Confidence 44489999999999999999983 3433 34448887653
No 17
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=20.62 E-value=71 Score=23.34 Aligned_cols=36 Identities=31% Similarity=0.730 Sum_probs=26.6
Q ss_pred CCCCCcccccccceeechHHHHHHHHcCCC--CCCCeeeeCCCC
Q 032415 83 DFVPDESAIKTDQIEVDKETLDMLEALGMN--EIPGLVRVDPVA 124 (141)
Q Consensus 83 nyvpe~S~ld~~~i~VD~~T~eMlk~l~~~--~~~~~~~~~~~~ 124 (141)
++||+--.|+.| +-++.||.||++ .||.++..+|..
T Consensus 13 ~lVPeH~vls~e------E~~~vLk~l~i~~~qLPkI~~~DPva 50 (80)
T COG2012 13 ELVPEHEVLSEE------EAKEVLKELGIEPEQLPKIKASDPVA 50 (80)
T ss_pred cccCceEEcCHH------HHHHHHHHhCCCHHHCCcccccChhH
Confidence 466766555433 457999999997 699999999943
Done!