Query 045274
Match_columns 156
No_of_seqs 15 out of 17
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 11:35:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045274.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045274hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11061 DUF2862: Protein of u 73.7 5.2 0.00011 28.5 3.4 33 110-142 29-61 (64)
2 PF00181 Ribosomal_L2: Ribosom 48.5 38 0.00083 23.5 4.1 35 109-143 33-68 (77)
3 COG3042 Hlx Putative hemolysin 48.4 24 0.00051 26.5 3.2 34 102-135 38-71 (85)
4 TIGR03606 non_repeat_PQQ dehyd 39.0 26 0.00056 32.1 2.6 26 125-150 408-433 (454)
5 PF11178 DUF2963: Protein of u 32.2 83 0.0018 20.7 3.5 34 113-146 11-46 (51)
6 PF07653 SH3_2: Variant SH3 do 31.5 88 0.0019 19.5 3.4 31 106-139 16-48 (55)
7 PF14076 DUF4258: Domain of un 29.0 94 0.002 19.6 3.3 44 94-139 25-68 (73)
8 PF03900 Porphobil_deamC: Porp 25.2 1.4E+02 0.0031 19.9 3.9 35 110-144 22-56 (74)
9 PF10614 CsgF: Type VIII secre 24.1 1.3E+02 0.0027 24.2 3.9 67 68-137 67-134 (142)
10 COG1412 Uncharacterized protei 24.0 63 0.0014 25.4 2.1 41 71-111 47-98 (136)
11 PF05789 Baculo_VP1054: Baculo 23.9 36 0.00079 30.6 0.9 29 7-35 3-31 (325)
12 PHA00006 D external scaffoldin 23.4 18 0.0004 29.3 -0.9 42 107-155 19-60 (151)
13 PF03480 SBP_bac_7: Bacterial 23.2 1.3E+02 0.0028 24.0 3.9 52 58-112 2-54 (286)
14 PRK02939 lipoprotein; Reviewed 22.9 78 0.0017 27.4 2.7 22 125-147 113-134 (236)
15 PF13356 DUF4102: Domain of un 22.3 77 0.0017 21.7 2.1 12 128-139 28-39 (89)
16 PF04698 Rab_eff_C: Rab effect 22.2 44 0.00096 33.0 1.2 19 124-144 199-217 (714)
17 PF06347 SH3_4: Bacterial SH3 20.9 1.5E+02 0.0032 18.5 3.0 34 106-142 19-52 (55)
No 1
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=73.67 E-value=5.2 Score=28.46 Aligned_cols=33 Identities=21% Similarity=0.421 Sum_probs=29.6
Q ss_pred ceeeEEEEecCCceEEEEEECCCCccceEEeec
Q 045274 110 KGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQ 142 (156)
Q Consensus 110 kG~LlEf~Kds~R~lLaVv~rpdGKKNW~v~DQ 142 (156)
.|.+..|+--.+..+=.||+=+||+++||--|.
T Consensus 29 ~g~I~~fKmtDG~giG~vv~~~ng~~~WFFedE 61 (64)
T PF11061_consen 29 IGTIKGFKMTDGSGIGVVVEFSNGSRTWFFEDE 61 (64)
T ss_pred cEEEEEEEEecCCcEEEEEEecCCceeEEchhh
Confidence 689999998889999999999999999997663
No 2
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 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 [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=48.47 E-value=38 Score=23.49 Aligned_cols=35 Identities=23% Similarity=0.518 Sum_probs=30.7
Q ss_pred hceeeEEEEecCCce-EEEEEECCCCccceEEeecc
Q 045274 109 QKGLLLEFKKDSDRV-LLAVAQRPDGKKNWMVYDQV 143 (156)
Q Consensus 109 qkG~LlEf~Kds~R~-lLaVv~rpdGKKNW~v~DQ~ 143 (156)
.+|.+++.+.|..|. -+|+|.-.||++.|+..-++
T Consensus 33 ~~g~V~~i~~DP~Rsa~iAlV~~~~g~~~yiiA~eg 68 (77)
T PF00181_consen 33 IKGIVIDIEYDPNRSAPIALVKYEDGEKRYIIAPEG 68 (77)
T ss_dssp EEEEEEEEEEETTTSSEEEEEEETTSEEEEEEEBTT
T ss_pred CcEEEEEEEecCCcCccEEEEEecCCcEEEEEeECC
Confidence 679999999999985 69999999999999987653
No 3
>COG3042 Hlx Putative hemolysin [General function prediction only]
Probab=48.42 E-value=24 Score=26.46 Aligned_cols=34 Identities=26% Similarity=0.271 Sum_probs=29.0
Q ss_pred hhhhhhhhceeeEEEEecCCceEEEEEECCCCcc
Q 045274 102 KLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKK 135 (156)
Q Consensus 102 k~~~~~LqkG~LlEf~Kds~R~lLaVv~rpdGKK 135 (156)
....-=.|+|=-||+.|+.+-...++-+-|||++
T Consensus 38 pAs~yC~~~GG~l~~~~~~~G~~~~~C~LPdGr~ 71 (85)
T COG3042 38 PASVYCAQQGGTLEAVKREDGGVVGMCVLPDGRI 71 (85)
T ss_pred HHHHHHHHhCCeeeeEEccCCCEEEEEECCCCcc
Confidence 3444557899999999999988999999999995
No 4
>TIGR03606 non_repeat_PQQ dehydrogenase, PQQ-dependent, s-GDH family. PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterized PQQ-dependent enzymes have multiple repeats of a sequence region described by pfam01011 (PQQ enzyme repeat), but this protein family in unusual in lacking that repeat. Below the noise cutoff are related proteins mostly from species that lack PQQ biosynthesis.
Probab=39.01 E-value=26 Score=32.06 Aligned_cols=26 Identities=19% Similarity=0.218 Sum_probs=22.1
Q ss_pred EEEEECCCCccceEEeeccccccCcc
Q 045274 125 LAVAQRPDGKKNWMVYDQVLVETPNA 150 (156)
Q Consensus 125 LaVv~rpdGKKNW~v~DQ~g~~~si~ 150 (156)
=.|++.|||..-|+++|.+|..+-+.
T Consensus 408 Rdv~~~pDg~~iy~~td~~g~~~~~~ 433 (454)
T TIGR03606 408 RDVIASPDGNVLYVATDNFGNVQKDD 433 (454)
T ss_pred EEEEECCCCCEEEEEEcCCCccccCC
Confidence 46899999999999999999876543
No 5
>PF11178 DUF2963: Protein of unknown function (DUF2963); InterPro: IPR021348 This family of proteins with unknown function appears to be restricted to Mollicutes.
Probab=32.24 E-value=83 Score=20.68 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=25.8
Q ss_pred eEEEEecCCceEEEEEECCCCccceEE--eeccccc
Q 045274 113 LLEFKKDSDRVLLAVAQRPDGKKNWMV--YDQVLVE 146 (156)
Q Consensus 113 LlEf~Kds~R~lLaVv~rpdGKKNW~v--~DQ~g~~ 146 (156)
.-||....+..+=-..-.||||.-|.+ +||+|..
T Consensus 11 I~eydp~Tg~~iK~t~Y~~DGktI~~I~Eyd~t~~~ 46 (51)
T PF11178_consen 11 ITEYDPQTGKKIKKTYYNPDGKTIKYIYEYDQTGKL 46 (51)
T ss_pred EEEECcccCcEeeeEEECCCCCEEEEEEEECCCCcE
Confidence 458888778888888889999865555 7887754
No 6
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=31.45 E-value=88 Score=19.51 Aligned_cols=31 Identities=29% Similarity=0.566 Sum_probs=20.4
Q ss_pred hhhhceeeEEEE--ecCCceEEEEEECCCCccceEE
Q 045274 106 QVLQKGLLLEFK--KDSDRVLLAVAQRPDGKKNWMV 139 (156)
Q Consensus 106 ~~LqkG~LlEf~--Kds~R~lLaVv~rpdGKKNW~v 139 (156)
=++++|=+|+.- ++.+-..++-. +|++-||=
T Consensus 16 Ls~~~Gd~i~v~~~~~~~~ww~~~~---~g~~G~~P 48 (55)
T PF07653_consen 16 LSFKKGDVIEVLGEKDDDGWWLGEN---NGRRGWFP 48 (55)
T ss_dssp -EB-TTEEEEEEEEECSTSEEEEEE---TTEEEEEE
T ss_pred eEEecCCEEEEEEeecCCCEEEEEE---CCcEEEEc
Confidence 357888888875 66666666655 78887764
No 7
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=29.05 E-value=94 Score=19.57 Aligned_cols=44 Identities=25% Similarity=0.325 Sum_probs=26.0
Q ss_pred cccccchhhhhhhhhhceeeEEEEecCCceEEEEEECCCCccceEE
Q 045274 94 SSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMV 139 (156)
Q Consensus 94 ~~gEllddk~~~~~LqkG~LlEf~Kds~R~lLaVv~rpdGKKNW~v 139 (156)
-+|+..+++-....-.--+.++..++.+ .|.||-.+++.+..++
T Consensus 25 ~~g~i~~~~~~~~~~~~~~~~~~~~~~~--~l~Vv~~~~~~~~~Vi 68 (73)
T PF14076_consen 25 ENGEIIEDYSDDKRGPCRLYIGGGKEGR--PLHVVIAPDGDPIVVI 68 (73)
T ss_pred hcCeEeeecCCCCCCCeEEEEEecCCCC--EEEEEEEECCCcEEEE
Confidence 5677776655444444445555555533 7888888888844333
No 8
>PF03900 Porphobil_deamC: Porphobilinogen deaminase, C-terminal domain; InterPro: IPR022418 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the C-terminal domain of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this alpha/beta domain consists of alpha-beta(3)-alpha in two layers []. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 3EQ1_B 3ECR_A 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A.
Probab=25.25 E-value=1.4e+02 Score=19.95 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=23.3
Q ss_pred ceeeEEEEecCCceEEEEEECCCCccceEEeeccc
Q 045274 110 KGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQVL 144 (156)
Q Consensus 110 kG~LlEf~Kds~R~lLaVv~rpdGKKNW~v~DQ~g 144 (156)
.|..-+++.|..=.+-|.+-.+||++..+-....|
T Consensus 22 iga~a~~~~~~~l~l~~~v~~~dG~~~~~~~~~~~ 56 (74)
T PF03900_consen 22 IGAYAKIEGDERLRLRAMVGSPDGSRIIIRVEITG 56 (74)
T ss_dssp EEEEEEEETTE-EEEEEEEE-TTSSSEEEEEEEEE
T ss_pred eeeEEEEcCCCEEEEEEEEECCCCCEEEEEEEEEc
Confidence 46677777552257778999999999555555555
No 9
>PF10614 CsgF: Type VIII secretion system (T8SS), CsgF protein; InterPro: IPR018893 Fimbriae are cell-surface protein polymers, of e.g. Escherichia coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp. and the controlling operon termed agf; however subsequent isolation of the homologous operon in E. coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix []. CsgF is one of three putative curli assembly factors appearing to act as a nucleator protein. Unlike eukaryotic amyloid formation, curli biogenesis is a productive pathway requiring a specific assembly machinery [].
Probab=24.05 E-value=1.3e+02 Score=24.15 Aligned_cols=67 Identities=15% Similarity=0.216 Sum_probs=50.7
Q ss_pred hhhHHHHHHHHHHHHhhhceeeeeeecccccchhhhhhhhhhce-eeEEEEecCCceEEEEEECCCCccce
Q 045274 68 HSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKG-LLLEFKKDSDRVLLAVAQRPDGKKNW 137 (156)
Q Consensus 68 ~slVdSVleEL~s~Rk~rr~~~s~ki~~gEllddk~~~~~LqkG-~LlEf~Kds~R~lLaVv~rpdGKKNW 137 (156)
.|-+|..-+.|.++==.+ ++..|..+++=||-.++|++.-| ..||+...+|-+++-+.++-.|+.-=
T Consensus 67 ~S~l~~F~~sLqsqlls~---l~~~i~~~~fGe~~~~~Gt~~~gdf~I~i~~~~g~l~v~I~D~~TGe~T~ 134 (142)
T PF10614_consen 67 LSALDRFTQSLQSQLLSQ---LSRDITQGIFGEDPQKPGTFTTGDFTIEIVNSDGGLVVNITDKNTGEVTT 134 (142)
T ss_pred CCHHHHHHHHHHHHHHHH---HHHHHHhccccCCCCCCceEEECCEEEEEEeCCCeEEEEEEeCCCccEEE
Confidence 456677777776654444 56667788888887788888765 67999999999999999998887543
No 10
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=24.05 E-value=63 Score=25.43 Aligned_cols=41 Identities=22% Similarity=0.428 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhhhceeeeeee-----------cccccchhhhhhhhhhce
Q 045274 71 VDSVMQELVAIRKRLRVFAKVKV-----------SSGELLEDKLENQVLQKG 111 (156)
Q Consensus 71 VdSVleEL~s~Rk~rr~~~s~ki-----------~~gEllddk~~~~~LqkG 111 (156)
=+.|++||+...+..|+.++.+| -++.-.||-+.+-+++-|
T Consensus 47 p~~Vi~EL~~l~~~~~~~~r~~ia~~~~er~~~~~~~~~aDe~i~~~a~~~~ 98 (136)
T COG1412 47 PSCVIRELEKLKRKHRGKARIAIALKYAERLECIHKGRYADECLLEAALKHG 98 (136)
T ss_pred hHHHHHHHHHHHHhcCchHHHHHHHHHhhccCccccCCChHHHHHHHHHHcC
Confidence 45799999999987666565322 225555888887777766
No 11
>PF05789 Baculo_VP1054: Baculovirus VP1054 protein; InterPro: IPR008416 This family consists of several VP1054 proteins from the Baculoviruses. VP1054 is a virus structural protein required for nucleocapsid assembly [].
Probab=23.94 E-value=36 Score=30.58 Aligned_cols=29 Identities=28% Similarity=0.417 Sum_probs=23.0
Q ss_pred ccccceeccCCCCcceeeeccccccchhh
Q 045274 7 NSCSMFRSAACPPLVSFKIQCCYYHFRSL 35 (156)
Q Consensus 7 n~CSi~r~~~~pp~~l~~~~~Rl~~lr~~ 35 (156)
|-|-.-|++.--|+-..+.|||+||+|+-
T Consensus 3 ~~cvs~k~~pykPi~~~k~qC~~HP~Ran 31 (325)
T PF05789_consen 3 NQCVSEKSTPYKPIKPTKTQCRIHPLRAN 31 (325)
T ss_pred cccchhcccCccccCCCCCCCCcCCCcCC
Confidence 45666677767788889999999999765
No 12
>PHA00006 D external scaffolding protein
Probab=23.38 E-value=18 Score=29.35 Aligned_cols=42 Identities=26% Similarity=0.488 Sum_probs=29.6
Q ss_pred hhhceeeEEEEecCCceEEEEEECCCCccceEEeeccccccCccccccC
Q 045274 107 VLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQVLVETPNAACSLG 155 (156)
Q Consensus 107 ~LqkG~LlEf~Kds~R~lLaVv~rpdGKKNW~v~DQ~g~~~si~~~~~~ 155 (156)
-+|+...|....| |--. -.|.|-|+++|.+--.--+.||-.|
T Consensus 19 liqasavldlted-dfdf------lt~dkvwiatdrsrarr~veacvyg 60 (151)
T PHA00006 19 LIQASAVLDLTED-DFDF------LTGDKVWIATDRSRARRCVEACVYG 60 (151)
T ss_pred HHHHhhhhccccc-hhhh------hccceeEEeechHHHHHHHHHHHhc
Confidence 4566666666655 2211 2478999999999888888888765
No 13
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=23.23 E-value=1.3e+02 Score=24.02 Aligned_cols=52 Identities=15% Similarity=0.201 Sum_probs=38.5
Q ss_pred ccCCCCccchhhhHHHHHHHHHHHHhhhceeeeeee-cccccchhhhhhhhhhcee
Q 045274 58 NRSGSQSCSVHSLVDSVMQELVAIRKRLRVFAKVKV-SSGELLEDKLENQVLQKGL 112 (156)
Q Consensus 58 ~h~~~~s~sv~slVdSVleEL~s~Rk~rr~~~s~ki-~~gEllddk~~~~~LqkG~ 112 (156)
+|.-...-..+.-++...||+...-..+ +..+| .+|+|.++.-.-..|+.|.
T Consensus 2 a~~~p~~~~~~~~~~~fa~~v~e~t~G~---v~i~v~~~g~lg~~~e~~~~v~~G~ 54 (286)
T PF03480_consen 2 AHVWPEGHPITQAVEKFAEEVEERTGGR---VKIEVFPAGQLGKEAEVLEAVQDGA 54 (286)
T ss_dssp EESSTTTSHHHHHHHHHHHHHHHHTTTS---EEEEEEETTSSSSHHHHHHHHHTTS
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHcCCe---EEEEEecCcccCCHHHHHHHHhCCC
Confidence 3444444555666788888888887777 88888 7888888877777777776
No 14
>PRK02939 lipoprotein; Reviewed
Probab=22.91 E-value=78 Score=27.36 Aligned_cols=22 Identities=18% Similarity=0.238 Sum_probs=19.0
Q ss_pred EEEEECCCCccceEEeecccccc
Q 045274 125 LAVAQRPDGKKNWMVYDQVLVET 147 (156)
Q Consensus 125 LaVv~rpdGKKNW~v~DQ~g~~~ 147 (156)
+=+++.|||+.+|- +|.+|+-.
T Consensus 113 Cql~~~~dg~l~~~-~nd~GfI~ 134 (236)
T PRK02939 113 CQLAELPSAGVSWE-TDDNGFVI 134 (236)
T ss_pred eEEEEccCCcEEEE-ECCCceEE
Confidence 66889999999998 88898753
No 15
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=22.28 E-value=77 Score=21.66 Aligned_cols=12 Identities=25% Similarity=0.548 Sum_probs=5.5
Q ss_pred EECCCCccceEE
Q 045274 128 AQRPDGKKNWMV 139 (156)
Q Consensus 128 v~rpdGKKNW~v 139 (156)
...|.|.|-|++
T Consensus 28 ~v~~~G~kt~~~ 39 (89)
T PF13356_consen 28 RVTPSGSKTFYF 39 (89)
T ss_dssp EE-TTS-EEEEE
T ss_pred EEEeCCCeEEEE
Confidence 334566666653
No 16
>PF04698 Rab_eff_C: Rab effector MyRIP/melanophilin C-terminus; InterPro: IPR006788 MOBP is abundantly expressed in central nervous system myelin, and shares several characteristics with myelin basic protein (MBP), in terms of regional distribution and function. MOBP has been shown to be essential for normal arrangement of the radial component in central nervous system myelin [, ].
Probab=22.24 E-value=44 Score=32.98 Aligned_cols=19 Identities=37% Similarity=0.697 Sum_probs=15.2
Q ss_pred EEEEEECCCCccceEEeeccc
Q 045274 124 LLAVAQRPDGKKNWMVYDQVL 144 (156)
Q Consensus 124 lLaVv~rpdGKKNW~v~DQ~g 144 (156)
+--|++-||| |||+.--+.
T Consensus 199 ~s~VLqSPDG--NWiALqs~~ 217 (714)
T PF04698_consen 199 ASPVLQSPDG--NWIALQSSQ 217 (714)
T ss_pred chhhccCCCC--CeeecccCC
Confidence 4569999999 999986555
No 17
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=20.94 E-value=1.5e+02 Score=18.47 Aligned_cols=34 Identities=15% Similarity=0.282 Sum_probs=24.9
Q ss_pred hhhhceeeEEEEecCCceEEEEEECCCCccceEEeec
Q 045274 106 QVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQ 142 (156)
Q Consensus 106 ~~LqkG~LlEf~Kds~R~lLaVv~rpdGKKNW~v~DQ 142 (156)
..|++|..++..+..+.- +- |+ .||..-|+-.++
T Consensus 19 ~~l~~g~~v~v~~~~~~W-~~-V~-~~g~~GWv~~~~ 52 (55)
T PF06347_consen 19 ARLEPGVPVRVIECRGGW-CK-VR-ADGRTGWVHKSL 52 (55)
T ss_pred EEECCCCEEEEEEccCCe-EE-EE-ECCeEEeEEeee
Confidence 678999999998774433 33 34 889999987654
Done!