Query psy5121
Match_columns 204
No_of_seqs 59 out of 61
Neff 2.0
Searched_HMMs 46136
Date Fri Aug 16 17:53:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4177|consensus 99.6 3E-17 6.5E-22 164.0 -2.3 105 49-170 833-937 (1143)
2 PF00791 ZU5: ZU5 domain; Int 95.8 0.016 3.4E-07 43.6 4.3 65 98-169 6-71 (103)
3 smart00218 ZU5 Domain present 73.3 6.6 0.00014 30.7 4.3 63 98-169 6-71 (104)
4 COG1385 Uncharacterized protei 51.7 9.6 0.00021 33.1 1.8 50 52-108 154-205 (246)
5 PRK13571 anthranilate synthase 38.8 18 0.0004 34.5 1.7 36 85-128 380-415 (506)
6 PRK11713 16S ribosomal RNA met 34.5 18 0.00039 30.2 0.8 15 98-112 181-195 (234)
7 PF04452 Methyltrans_RNA: RNA 33.6 17 0.00037 30.0 0.5 10 98-107 178-187 (225)
8 TIGR00046 RNA methyltransferas 30.9 22 0.00048 29.8 0.8 12 97-108 187-198 (240)
9 PF10461 Peptidase_S68: Peptid 27.6 69 0.0015 21.6 2.5 26 69-94 9-35 (35)
10 TIGR00553 pabB aminodeoxychori 26.7 38 0.00081 30.7 1.5 36 84-127 215-250 (328)
11 TIGR00564 trpE_most anthranila 26.3 32 0.00068 32.2 1.0 36 84-127 336-371 (454)
12 cd05766 IgC_MHC_II_beta Class 26.0 1.7E+02 0.0037 21.1 4.6 32 126-177 14-45 (94)
13 KOG1329|consensus 25.8 48 0.001 34.7 2.3 59 29-94 806-870 (887)
14 PRK09070 hypothetical protein; 25.1 38 0.00082 31.9 1.3 36 84-127 327-362 (447)
15 TIGR01823 PabB-fungal aminodeo 24.2 50 0.0011 32.9 2.0 42 84-127 616-657 (742)
16 PRK05940 anthranilate synthase 23.9 46 0.00099 31.6 1.6 34 86-127 335-368 (463)
17 PF02978 SRP_SPB: Signal pepti 23.2 2 4.4E-05 32.9 -6.2 29 52-80 52-80 (104)
18 PRK15465 pabB aminodeoxychoris 22.8 46 0.001 31.6 1.4 36 85-128 335-370 (453)
19 cd05889 Ig1_DNAM-1_like First 21.5 73 0.0016 23.7 2.0 24 103-131 70-93 (96)
20 TIGR02058 lin0512_fam conserve 20.1 1.1E+02 0.0024 24.8 2.9 62 108-178 30-94 (116)
No 1
>KOG4177|consensus
Probab=99.61 E-value=3e-17 Score=163.95 Aligned_cols=105 Identities=37% Similarity=0.461 Sum_probs=93.5
Q ss_pred cccChhhhhhhcCCCCCCCCCcCCCCceEEEEcCCCCceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCceee
Q psy5121 49 WPVNYKGILSVLTILDMPPPVEADPSRLTRILTMDFPHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTKK 128 (204)
Q Consensus 49 Wp~~~e~il~~l~~EeL~slEel~~kRI~RIiT~DFPqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTKk 128 (204)
|-+.+-+.=..--.+.|.+.++|.++|+|||+|.| |++|+++.+|||||. |+.+|+||++||++++||+
T Consensus 833 ~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~~---------~v~~~~~~~g~~~~~--~~~~~~~~~~f~~~~~~~~ 901 (1143)
T KOG4177|consen 833 WKEHDCNYGEDKLYEILNSAEELDTKRICRIITSD---------RVRQEYLASGPEGGV--STLVPLVQAVFPENALTKR 901 (1143)
T ss_pred HhhhhhccCcchhhhccchHHHhcccchhhHHhhh---------hhccccccccCCCCc--CcccceehhhcCCCcchHH
Confidence 76644333333345677799999999999999999 999999999999999 9999999999999999999
Q ss_pred eEEEEEeeecCCCCCCChhhHhhhhccCCCcceeeEEEEecc
Q psy5121 129 IKVGLQVNLFKPRKNVPPAALKKITVNHIPKKKRFSLVWVGG 170 (204)
Q Consensus 129 IrVgLQaQPI~P~qpV~de~vrki~GN~a~~spivTlEpr~~ 170 (204)
||++||+|| ++.++++++.||++++++|+|+|+|+-
T Consensus 902 ~r~~~~~~~------~~~~~~~~~~~~~~~~~~i~~~e~r~~ 937 (1143)
T KOG4177|consen 902 IRVSLQAQP------VPLEVVTKLLGNKATFSPIVTVEPRRR 937 (1143)
T ss_pred HHHHHhccc------ccHHHHHHhcCCcccccceeeecchHH
Confidence 999999977 679999999999999999999999963
No 2
>PF00791 ZU5: ZU5 domain; InterPro: IPR000906 This is a domain of unknown function, present in ZO-1 and Unc5-like netrin receptors. It is also found in different variants of ankyrin, which are responsible for attaching integral membrane proteins to cytoskeletal elements.; PDB: 4D8O_A 3G5B_A 3UD2_C 3KBT_D 3UD1_A 3KBU_D 3F59_A 2KXS_A 2KXR_A.
Probab=95.78 E-value=0.016 Score=43.55 Aligned_cols=65 Identities=15% Similarity=0.129 Sum_probs=40.9
Q ss_pred eeeecCCCceEEeeeecceeEecCCCCceeeeEEEEEeeecCCCCCCChhhHhhhhccC-CCcceeeEEEEec
Q psy5121 98 VHAIGPEGGMVSSSVVPQVQAVFPQGALTKKIKVGLQVNLFKPRKNVPPAALKKITVNH-IPKKKRFSLVWVG 169 (204)
Q Consensus 98 ~~~IGPEGG~lsSsvVPqVQA~FPeGALTKkIrVgLQaQPI~P~qpV~de~vrki~GN~-a~~spivTlEpr~ 169 (204)
...||.+||.|. .--..|.-.+|+||+.+..+..++...... .+ .... +.++ +-.||+|.+-|.+
T Consensus 6 ~~~v~~~GG~L~-l~~~gv~L~IPpGAv~~~~~~~i~l~~~~~---~~-~~~~--l~~~e~llSpvv~~gP~g 71 (103)
T PF00791_consen 6 SGIVDHEGGRLR-LPESGVSLSIPPGAVPKGTRIEIYLAVPRD---DP-DRPP--LEEGETLLSPVVECGPSG 71 (103)
T ss_dssp EEEE-TT-EEEE-STTTTEEEEE-TTSSSTTEEEEEEEEECSG---CS-SGGG--TTTTEEESSTCEEEESTT
T ss_pred EEEEeCCCcEEE-eCCCCEEEEECCCcCCCCCEEEEEEEeccc---cc-cccc--cCCCCEEeCCEEEEECCC
Confidence 467999999999 444689999999999987777776544321 00 1111 3333 5578888887654
No 3
>smart00218 ZU5 Domain present in ZO-1 and Unc5-like netrin receptors. Domain of unknown function.
Probab=73.31 E-value=6.6 Score=30.66 Aligned_cols=63 Identities=14% Similarity=0.164 Sum_probs=41.4
Q ss_pred eeeecCCCceEEeeeecceeEecCCCCce--eeeEEEEEe-eecCCCCCCChhhHhhhhccCCCcceeeEEEEec
Q psy5121 98 VHAIGPEGGMVSSSVVPQVQAVFPQGALT--KKIKVGLQV-NLFKPRKNVPPAALKKITVNHIPKKKRFSLVWVG 169 (204)
Q Consensus 98 ~~~IGPEGG~lsSsvVPqVQA~FPeGALT--KkIrVgLQa-QPI~P~qpV~de~vrki~GN~a~~spivTlEpr~ 169 (204)
..+++..||.|...- ..|.-..|+||+. +++.+.|=+ |..+=..+ .....+-.||+|..=|.+
T Consensus 6 ~~~~d~~GG~L~~~~-~Gv~L~IPpgAi~~~~~~~iyl~v~~~~~~~p~--------l~~~e~llSpvV~cGP~G 71 (104)
T smart00218 6 SGTFDARGGRLRGPR-TGVRLIIPPGAIPQGTRYTCYLVVHKTLSTPPP--------LEEGETLLSPVVECGPHG 71 (104)
T ss_pred EEEEeCCCCEEEeCC-CCeEEEeCCCCCCCCCEEEEEEEEecCcCCCCc--------cCCCcEeeCCeEEECCCC
Confidence 468999999999988 9999999999999 555566532 11100011 122335568888877743
No 4
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.65 E-value=9.6 Score=33.05 Aligned_cols=50 Identities=22% Similarity=0.202 Sum_probs=27.4
Q ss_pred ChhhhhhhcCCCC--CCCCCcCCCCceEEEEcCCCCceeEEEeeeeeeeeeecCCCceE
Q psy5121 52 NYKGILSVLTILD--MPPPVEADPSRLTRILTMDFPHYFAVVSRVKQEVHAIGPEGGMV 108 (204)
Q Consensus 52 ~~e~il~~l~~Ee--L~slEel~~kRI~RIiT~DFPqYFAVVSRIrQE~~~IGPEGG~l 108 (204)
+.+++++.++.++ .--+++.++.....+... -......-.-.||||||--
T Consensus 154 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~i~iiIGPEGGfs 205 (246)
T COG1385 154 SLKELLKEIDDEDALKLIYEEKAKEGLLALPLL-------EALPEGKVLLIIGPEGGFS 205 (246)
T ss_pred hHHHHHHhcccchhhhheeccccccccccchhh-------hcccCCcEEEEECCCCCCC
Confidence 5566666666444 344455555554444432 1122344566899999953
No 5
>PRK13571 anthranilate synthase component I; Provisional
Probab=38.75 E-value=18 Score=34.52 Aligned_cols=36 Identities=33% Similarity=0.563 Sum_probs=24.9
Q ss_pred CceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCceee
Q psy5121 85 PHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTKK 128 (204)
Q Consensus 85 PqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTKk 128 (204)
++-.-++|+|.-+..- | -+.+--+++.||.||+|--
T Consensus 380 ~~V~HL~S~V~g~L~~----~----~~~~d~l~a~fP~gsvtGa 415 (506)
T PRK13571 380 SHVMHLVSTVTGELAE----G----RTALDAVTACFPAGTLSGA 415 (506)
T ss_pred CceEEEeeEEEEEECC----C----CCHHHHHHHhCCCcccCCC
Confidence 5667788888755531 1 1345568999999999863
No 6
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=34.53 E-value=18 Score=30.22 Aligned_cols=15 Identities=40% Similarity=0.849 Sum_probs=10.7
Q ss_pred eeeecCCCceEEeee
Q psy5121 98 VHAIGPEGGMVSSSV 112 (204)
Q Consensus 98 ~~~IGPEGG~lsSsv 112 (204)
.-+||||||--...+
T Consensus 181 ~viIGPEGGfs~~Ei 195 (234)
T PRK11713 181 LLLIGPEGGFSPEEI 195 (234)
T ss_pred EEEECCCCCCCHHHH
Confidence 468999999654433
No 7
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=33.61 E-value=17 Score=30.01 Aligned_cols=10 Identities=60% Similarity=1.122 Sum_probs=4.9
Q ss_pred eeeecCCCce
Q psy5121 98 VHAIGPEGGM 107 (204)
Q Consensus 98 ~~~IGPEGG~ 107 (204)
.-+||||||-
T Consensus 178 ~i~IGPEGGf 187 (225)
T PF04452_consen 178 AIIIGPEGGF 187 (225)
T ss_dssp EEEE--TT--
T ss_pred EEEECCCCCC
Confidence 5689999995
No 8
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=30.89 E-value=22 Score=29.85 Aligned_cols=12 Identities=58% Similarity=0.925 Sum_probs=9.2
Q ss_pred eeeeecCCCceE
Q psy5121 97 EVHAIGPEGGMV 108 (204)
Q Consensus 97 E~~~IGPEGG~l 108 (204)
=.-+||||||--
T Consensus 187 v~~~IGPEGGfs 198 (240)
T TIGR00046 187 IVIIIGPEGGFS 198 (240)
T ss_pred EEEEECCCCCCC
Confidence 347899999953
No 9
>PF10461 Peptidase_S68: Peptidase S68; InterPro: IPR019502 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry contains serine peptidases belonging to MEROPS peptidase family S68 (PIDD auto-processing protein, clan S-). These proteins are known as Pidd (short for p53-induced protein with a death domain) proteins. Pidd forms a complex with Raidd and procaspase-2 that is known as the 'Piddosome'. The Piddosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis.
Probab=27.63 E-value=69 Score=21.61 Aligned_cols=26 Identities=23% Similarity=0.197 Sum_probs=16.5
Q ss_pred CcCCCCc-eEEEEcCCCCceeEEEeee
Q psy5121 69 VEADPSR-LTRILTMDFPHYFAVVSRV 94 (204)
Q Consensus 69 Eel~~kR-I~RIiT~DFPqYFAVVSRI 94 (204)
|+-.++| -...-+.-..++|.||||+
T Consensus 9 ~~~~~~~s~~A~C~V~hFSWFlvVsRp 35 (35)
T PF10461_consen 9 ERGSKKRSHWACCSVPHFSWFLVVSRP 35 (35)
T ss_pred hccCCccceeEEecccccEEEEEEecC
Confidence 3444555 3444455566889999995
No 10
>TIGR00553 pabB aminodeoxychorismate synthase, component I, bacterial clade. Members of this family, aminodeoxychorismate synthase, component I (PabB), were designated para-aminobenzoate synthase component I until it was recognized that PabC, a lyase, completes the pathway of PABA synthesis. This family is closely related to anthranilate synthase component I (trpE), and both act on chorismate. The clade of PabB enzymes represented by this model includes sequences from Gram-positive and alpha and gamma Proteobacteria as well as Chlorobium, Nostoc, Fusobacterium and Arabidopsis. A closely related clade of fungal PabB enzymes is identified by TIGR01823, while another bacterial clade of potential PabB enzymes is more closely related to TrpE (TIGR01824).
Probab=26.65 E-value=38 Score=30.69 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=25.6
Q ss_pred CCceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCcee
Q psy5121 84 FPHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTK 127 (204)
Q Consensus 84 FPqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTK 127 (204)
|+.-+-++|+|+-+.. +| -++.--++|.||.||+|-
T Consensus 215 ~~~v~HL~S~v~g~L~----~~----~~~~~ll~alfP~gsVtG 250 (328)
T TIGR00553 215 YPTVHQLVSTITARLR----ED----LTLSDLFRALFPGGSITG 250 (328)
T ss_pred eCcEEEEEEEEEEEEC----CC----CCHHHHHHHhCCCCccCC
Confidence 4556778888887663 22 135566799999999995
No 11
>TIGR00564 trpE_most anthranilate synthase component I, non-proteobacterial lineages. A second family of TrpE enzymes is modelled by TIGR00565. The breaking of the TrpE family into these diverse models allows for the separation of the models for the related enzyme, PabB.
Probab=26.27 E-value=32 Score=32.18 Aligned_cols=36 Identities=22% Similarity=0.521 Sum_probs=24.3
Q ss_pred CCceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCcee
Q psy5121 84 FPHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTK 127 (204)
Q Consensus 84 FPqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTK 127 (204)
|++-+-+||+|.-+..- + .+.+--+++.||.||+|-
T Consensus 336 ~~~v~HL~S~v~g~L~~---~-----~~~~d~l~a~~P~gsvtG 371 (454)
T TIGR00564 336 YSHVMHIVSTVEGRLKD---G-----LTAIDALRATFPAGTVSG 371 (454)
T ss_pred cCcEEEEEEEEEEEECC---C-----CCHHHHHHHhCCCCCCCC
Confidence 55666788888754321 1 234556889999999985
No 12
>cd05766 IgC_MHC_II_beta Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain. IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome be
Probab=25.99 E-value=1.7e+02 Score=21.14 Aligned_cols=32 Identities=19% Similarity=0.317 Sum_probs=20.5
Q ss_pred eeeeEEEEEeeecCCCCCCChhhHhhhhccCCCcceeeEEEEeccceeeecc
Q psy5121 126 TKKIKVGLQVNLFKPRKNVPPAALKKITVNHIPKKKRFSLVWVGGGATVRSG 177 (204)
Q Consensus 126 TKkIrVgLQaQPI~P~qpV~de~vrki~GN~a~~spivTlEpr~~~~~~~~~ 177 (204)
.++..+.-+|.-.+| +-+++.|.++|..+..+
T Consensus 14 ~~~~~L~C~~~gFyP--------------------~~i~v~W~~~g~~~~~~ 45 (94)
T cd05766 14 SHPHLLVCHVWGFYP--------------------PEITVKWFKNGQEETEG 45 (94)
T ss_pred CCCeEEEEEEeeecC--------------------CCCEEEEEECCeecCCC
Confidence 455666667766666 23567777777766655
No 13
>KOG1329|consensus
Probab=25.84 E-value=48 Score=34.66 Aligned_cols=59 Identities=24% Similarity=0.294 Sum_probs=31.8
Q ss_pred cceeeeeeCCeeeeEee------ecccccChhhhhhhcCCCCCCCCCcCCCCceEEEEcCCCCceeEEEeee
Q psy5121 29 IEQVKLCYPGSVNVSVD------IDQWPVNYKGILSVLTILDMPPPVEADPSRLTRILTMDFPHYFAVVSRV 94 (204)
Q Consensus 29 ~~~~~~~~~~~~~~~~~------~~~Wp~~~e~il~~l~~EeL~slEel~~kRI~RIiT~DFPqYFAVVSRI 94 (204)
.+++.+|||-++-.+-. ++.-|.+--++...+ ..-.+| ..-+|=.+.+||+||-.=++.
T Consensus 806 y~~~f~~yP~~~~~~g~~~~~~~~~~~pd~~~~~~~~~----~~~~~~---~lt~~g~l~~fp~~~~~~~~~ 870 (887)
T KOG1329|consen 806 YEGHFRCYPIDVVRTGKVTELPGDETFPDTLGKIIGSK----SDALPE---NLTTRGFLVSFPLYFLCKESL 870 (887)
T ss_pred hhceEEEcccccccCcceeecCCccccccccccccccc----cccCCc---cccccceeeeeeeEEeehhhc
Confidence 68899999976654432 222222222222221 112222 222377889999999765443
No 14
>PRK09070 hypothetical protein; Validated
Probab=25.12 E-value=38 Score=31.91 Aligned_cols=36 Identities=31% Similarity=0.569 Sum_probs=25.0
Q ss_pred CCceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCcee
Q psy5121 84 FPHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTK 127 (204)
Q Consensus 84 FPqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTK 127 (204)
|++-.-++|+|+-+..- | .+.+--+++.||.||+|-
T Consensus 327 ~~~V~HL~S~V~g~L~~----~----~~~~d~l~alfP~gsvtG 362 (447)
T PRK09070 327 YAHVHHIVSNVRGRLRD----G----VTPGEVIRAVFPGGTITG 362 (447)
T ss_pred cCcEEEEEEEEEEEECC----C----CCHHHHHHHcCCCCccCC
Confidence 45666778888765432 1 134567789999999985
No 15
>TIGR01823 PabB-fungal aminodeoxychorismate synthase, fungal clade. This model represents the fungal clade of a para-aminobenzoate synthesis enzyme, aminodeoxychorismate synthase, which acts on chorismate in a pathway that yields PABA, a precursor of folate.
Probab=24.21 E-value=50 Score=32.90 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=25.7
Q ss_pred CCceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCcee
Q psy5121 84 FPHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTK 127 (204)
Q Consensus 84 FPqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTK 127 (204)
|++-+-+||.++-+...- - ++.-..+.+--+.|.||.||+|-
T Consensus 616 ~~~V~hLvS~v~g~l~~~-~-~~~~~~~~~d~l~a~~P~gsvtG 657 (742)
T TIGR01823 616 HATVYQLVSVVKAHGLTS-A-SKKTRYSGIDVLKHSLPPGSMTG 657 (742)
T ss_pred cCCeEEEeeEEEEEECCC-C-CcccccCHHHHHHHhCCCccccC
Confidence 556667778877664321 0 11112234566789999999985
No 16
>PRK05940 anthranilate synthase component I-like protein; Validated
Probab=23.89 E-value=46 Score=31.64 Aligned_cols=34 Identities=26% Similarity=0.516 Sum_probs=22.1
Q ss_pred ceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCcee
Q psy5121 86 HYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTK 127 (204)
Q Consensus 86 qYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTK 127 (204)
+=+-+||+|+-+..- + -+.+--++|.||.||+|-
T Consensus 335 ~V~HLvS~V~G~L~~---~-----~~~~dll~al~P~gsvtG 368 (463)
T PRK05940 335 HVIHLVSNVVGTLQP---N-----RDAIDLIRALFPGGTITG 368 (463)
T ss_pred ceEEEEeEEEEEECC---C-----CCHHHHHHHhCCCCcCCC
Confidence 445577777654421 0 125567899999999985
No 17
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=23.23 E-value=2 Score=32.87 Aligned_cols=29 Identities=24% Similarity=0.266 Sum_probs=25.5
Q ss_pred ChhhhhhhcCCCCCCCCCcCCCCceEEEE
Q psy5121 52 NYKGILSVLTILDMPPPVEADPSRLTRIL 80 (204)
Q Consensus 52 ~~e~il~~l~~EeL~slEel~~kRI~RIi 80 (204)
.|+.|++..+++|++..+-+...|+.||.
T Consensus 52 ~~~~Ii~SMT~~Er~~p~ll~~sR~~RIA 80 (104)
T PF02978_consen 52 RMEAIIDSMTPEERDNPKLLNESRRRRIA 80 (104)
T ss_dssp HHHHHHTTSBHHHHHCGGGHHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHhCccccchHHHHHHH
Confidence 58899999999999999999888888873
No 18
>PRK15465 pabB aminodeoxychorismate synthase subunit I; Provisional
Probab=22.79 E-value=46 Score=31.58 Aligned_cols=36 Identities=22% Similarity=0.376 Sum_probs=23.7
Q ss_pred CceeEEEeeeeeeeeeecCCCceEEeeeecceeEecCCCCceee
Q psy5121 85 PHYFAVVSRVKQEVHAIGPEGGMVSSSVVPQVQAVFPQGALTKK 128 (204)
Q Consensus 85 PqYFAVVSRIrQE~~~IGPEGG~lsSsvVPqVQA~FPeGALTKk 128 (204)
++-+-+||+|.-+..- | -+.+--++|.||.||+|--
T Consensus 335 ~~V~HLvS~V~g~L~~----~----~~~~d~l~a~fP~gsvtGa 370 (453)
T PRK15465 335 PAVHHLVSTITARLPE----Q----LHASDLLRAAFPGGSITGA 370 (453)
T ss_pred CCEEEeEeEEEEEECC----C----CCHHHHHHHcCCCCccCCc
Confidence 4456677777655432 1 1245568999999999963
No 19
>cd05889 Ig1_DNAM-1_like First immunoglobulin (Ig) domain of DNAX accessory molecule 1 (DNAM-1, also known as CD226) and similar proteins. Ig1_DNAM-1_like: domain similar to the first immunoglobulin (Ig) domain of DNAX accessory molecule 1 (DNAM-1, also known as CD226). DNAM-1 is a transmembrane protein having two Ig-like domains. It is an adhesion molecule which plays a part in tumor-directed cytotoxicity and adhesion in natural killer (NK) cells and T lymphocytes. It has been shown to regulate the NK cell killing of several tumor types, including myeloma cells and ovarian carcinoma cells. DNAM-1 interacts specifically with poliovirus receptor (PVR; CD155) and nectin -2 (CD211), other members of the Ig superfamily. DNAM-1 is expressed in most peripheral T cells, NK cells, monocytes and a subset of B lymphocytes.
Probab=21.50 E-value=73 Score=23.67 Aligned_cols=24 Identities=33% Similarity=0.610 Sum_probs=17.8
Q ss_pred CCCceEEeeeecceeEecCCCCceeeeEE
Q psy5121 103 PEGGMVSSSVVPQVQAVFPQGALTKKIKV 131 (204)
Q Consensus 103 PEGG~lsSsvVPqVQA~FPeGALTKkIrV 131 (204)
.|.|.-.-.+ +.||.|-.+|+|+|
T Consensus 70 ~D~G~Y~C~~-----~t~P~g~~~~~i~~ 93 (96)
T cd05889 70 EDVGLYCCSL-----VTYPQGSWEKVIEV 93 (96)
T ss_pred ccCEEEEEEE-----EeCCCCCeEEEEEE
Confidence 4455555543 58999999999998
No 20
>TIGR02058 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus.
Probab=20.12 E-value=1.1e+02 Score=24.84 Aligned_cols=62 Identities=16% Similarity=0.283 Sum_probs=40.6
Q ss_pred EEeeeecceeEecCCCC---ceeeeEEEEEeeecCCCCCCChhhHhhhhccCCCcceeeEEEEeccceeeeccc
Q psy5121 108 VSSSVVPQVQAVFPQGA---LTKKIKVGLQVNLFKPRKNVPPAALKKITVNHIPKKKRFSLVWVGGGATVRSGE 178 (204)
Q Consensus 108 lsSsvVPqVQA~FPeGA---LTKkIrVgLQaQPI~P~qpV~de~vrki~GN~a~~spivTlEpr~~~~~~~~~~ 178 (204)
|+.+-+|-+..+||-+- ..=.+++|.| .|.+.|+-|.+++++=- -.+|++-+.||-.++||-
T Consensus 30 I~hnsipg~~~~~~~~~~~~M~v~V~igVp----~p~e~vD~e~v~~~~Py-----G~~~v~vv~GGL~v~sGi 94 (116)
T TIGR02058 30 IASNSMPGIWESLPDSSLNEMIVEVKLAVP----YDLDQLDEDKVKAIIPY-----GTVTVEVEDGGMITSSGI 94 (116)
T ss_pred HhhccchhHHHhcCCCChhheEEEEEEECC----CchHhcCHHHHHHhCCC-----CeeEEEEEcCCeEcccCc
Confidence 34556676666777543 3333444444 25455888888887643 335899999999999873
Done!