Query psy1573
Match_columns 104
No_of_seqs 101 out of 445
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 19:56:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1573.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1573hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2667|consensus 100.0 1.7E-36 3.6E-41 239.6 12.5 104 1-104 270-375 (379)
2 PF07970 COPIIcoated_ERV: Endo 100.0 6.6E-35 1.4E-39 216.7 8.3 88 1-89 134-222 (222)
3 PF10399 UCR_Fe-S_N: Ubiquitin 61.0 2.1 4.5E-05 24.1 -0.5 31 61-91 8-38 (41)
4 KOG4085|consensus 57.7 9.3 0.0002 27.5 2.2 25 66-90 26-51 (175)
5 PF11888 DUF3408: Protein of u 53.9 22 0.00048 24.4 3.6 37 64-100 86-123 (136)
6 PF01102 Glycophorin_A: Glycop 51.8 8.5 0.00019 26.5 1.2 17 85-101 78-94 (122)
7 PF05365 UCR_UQCRX_QCR9: Ubiqu 44.0 18 0.00038 21.5 1.6 30 72-101 14-43 (55)
8 TIGR03786 strep_pil_rpt strept 40.9 81 0.0018 19.0 4.5 31 23-64 11-41 (64)
9 PF00673 Ribosomal_L5_C: ribos 37.4 40 0.00087 21.8 2.7 23 55-77 1-23 (95)
10 PF11118 DUF2627: Protein of u 36.2 18 0.0004 23.0 0.9 22 67-88 40-61 (77)
11 PF07413 Herpes_UL37_2: Betahe 34.5 41 0.00089 26.3 2.7 43 58-100 228-273 (276)
12 KOG2014|consensus 32.3 13 0.00028 29.7 -0.3 11 73-83 286-296 (331)
13 PF02439 Adeno_E3_CR2: Adenovi 29.6 36 0.00077 18.9 1.2 29 73-101 4-32 (38)
14 PF00996 GDI: GDP dissociation 28.8 46 0.00099 27.5 2.2 26 65-90 232-257 (438)
15 PF05931 AgrD: Staphylococcal 27.9 32 0.00069 19.7 0.9 24 67-90 7-33 (45)
16 PRK08156 type III secretion sy 26.6 72 0.0016 25.7 2.9 30 67-96 174-203 (361)
17 TIGR01404 FlhB_rel_III type II 26.2 74 0.0016 25.3 2.9 29 67-95 178-206 (342)
18 COG3817 Predicted membrane pro 25.4 47 0.001 26.2 1.6 36 64-99 163-198 (313)
19 COG0094 RplE Ribosomal protein 24.9 77 0.0017 23.3 2.6 25 54-78 83-107 (180)
20 PF10661 EssA: WXG100 protein 23.8 34 0.00073 24.0 0.6 13 81-93 129-141 (145)
21 PRK09108 type III secretion sy 23.7 87 0.0019 25.1 2.9 30 67-96 181-210 (353)
22 COG5056 ARE1 Acyl-CoA choleste 23.7 74 0.0016 26.8 2.6 33 63-95 298-330 (512)
23 PRK12721 secretion system appa 23.7 88 0.0019 25.0 2.9 30 67-96 179-208 (349)
24 smart00794 AgrD Staphylococcal 23.5 44 0.00096 19.2 0.9 20 71-90 14-33 (45)
25 PRK00010 rplE 50S ribosomal pr 23.4 94 0.002 22.6 2.8 25 54-78 83-107 (179)
26 COG3765 WzzB Chain length dete 23.2 55 0.0012 26.4 1.7 40 48-89 298-337 (347)
27 KOG1652|consensus 23.0 57 0.0012 24.0 1.6 28 76-103 58-85 (183)
28 PF09881 DUF2108: Predicted me 22.8 65 0.0014 20.3 1.6 19 66-84 2-20 (72)
29 PRK12468 flhB flagellar biosyn 22.6 94 0.002 25.3 2.9 30 67-96 186-215 (386)
30 PF06459 RR_TM4-6: Ryanodine R 22.1 51 0.0011 25.6 1.3 15 65-79 250-264 (274)
31 PF11688 DUF3285: Protein of u 22.0 35 0.00076 19.5 0.3 21 61-81 17-37 (45)
32 PF15103 G0-G1_switch_2: G0/G1 21.4 33 0.00072 23.0 0.1 23 77-99 28-50 (102)
33 TIGR00328 flhB flagellar biosy 21.4 1E+02 0.0022 24.6 2.9 29 67-95 179-207 (347)
34 PF02061 Lambda_CIII: Lambda P 21.3 1.2E+02 0.0025 17.3 2.3 17 86-102 19-35 (45)
35 PRK04219 rpl5p 50S ribosomal p 20.5 1.1E+02 0.0025 22.3 2.8 25 54-78 66-90 (177)
36 KOG4405|consensus 20.3 53 0.0012 27.7 1.1 27 65-91 286-312 (547)
37 PF06143 Baculo_11_kDa: Baculo 20.2 64 0.0014 20.9 1.3 37 60-98 26-62 (84)
No 1
>KOG2667|consensus
Probab=100.00 E-value=1.7e-36 Score=239.60 Aligned_cols=104 Identities=36% Similarity=0.594 Sum_probs=95.7
Q ss_pred CceeEEEEEEEeeEEcC-CceEEEEeeeEEEEEEEeecCCCCCCceeEEEEEeccceEEEEEeeeccHHHHHHHHHhhhc
Q psy1573 1 MLFQYFIDVVPTDVDTM-FTTLRTYQYSAKELSRVIDHDVGSHGMSGIFFKYNTNALKVIVKETRDSFLNFFIRLSGVLG 79 (104)
Q Consensus 1 ~~~~YflkvVPT~y~~~-~~~~~t~QYSvt~~~~~~~~~~~~~~~PGIfF~Yd~sPi~v~~~~~~~s~~~flt~lcaIiG 79 (104)
.+|+||+|||||.|++. +..+.|||||||++++...+..+..++|||||+||+|||+|+++|+|.||+|||||+|||||
T Consensus 270 ~~~~Yf~KvVPT~y~~~~~~~~~T~QysVt~~~~~~~~~~~~~~~PGifF~YelSPl~V~v~E~r~sf~~Flt~lCAIiG 349 (379)
T KOG2667|consen 270 TTFQYFLKVVPTVYKYKSGRVIDTNQYSVTEYEYVLHSHRAKSGIPGIFFKYELSPLMVKVTEERQSFSHFLTRLCAIIG 349 (379)
T ss_pred cceeeEEEEcceEEEeecCceecceeeeeeeeEEeccccccccCCCeEEEEEecCceEEEEEeccccHHHHHHHHHHHhc
Confidence 37999999999999954 56899999999999999875555669999999999999999999999999999999999999
Q ss_pred ceeehhhhhHHHHHHHHHHHh-hhcC
Q psy1573 80 GVYIVTGTCSISQGALVEYFR-AMEM 104 (104)
Q Consensus 80 Gvf~v~g~id~~~~~~~~~~~-k~~~ 104 (104)
|+||++||+|++++++.+.++ |.++
T Consensus 350 Gvftvagiid~~~~~~~~~i~~k~~~ 375 (379)
T KOG2667|consen 350 GVFTVAGILDSLLYHILELIKGKIAL 375 (379)
T ss_pred ceeehHHHHHHHHHHHHHHHhcchhh
Confidence 999999999999999999998 6653
No 2
>PF07970 COPIIcoated_ERV: Endoplasmic reticulum vesicle transporter ; InterPro: IPR012936 This domain occurs in many hypothetical proteins, and also two partially characterised proteins. One of these proteins, PTX1 Q96RQ1 from SWISSPROT, is a homeodomain-containing transcription factor involved in regulating all pituitary hormone genes []. This protein is down regulated in prostate carcinoma []. The other protein, ERGIC-32 Q969X5 from SWISSPROT, is involved in protein transport from the ER to the Golgi [].
Probab=100.00 E-value=6.6e-35 Score=216.70 Aligned_cols=88 Identities=42% Similarity=0.820 Sum_probs=81.7
Q ss_pred CceeEEEEEEEeeEEcCCc-eEEEEeeeEEEEEEEeecCCCCCCceeEEEEEeccceEEEEEeeeccHHHHHHHHHhhhc
Q psy1573 1 MLFQYFIDVVPTDVDTMFT-TLRTYQYSAKELSRVIDHDVGSHGMSGIFFKYNTNALKVIVKETRDSFLNFFIRLSGVLG 79 (104)
Q Consensus 1 ~~~~YflkvVPT~y~~~~~-~~~t~QYSvt~~~~~~~~~~~~~~~PGIfF~Yd~sPi~v~~~~~~~s~~~flt~lcaIiG 79 (104)
++|+||||||||+|...++ ..+|||||||++.+.++... +.++|||||+||||||+|+++|+|+||+|||++||||||
T Consensus 134 ~~~~YflkvVPT~y~~~~~~~~~t~qYsvt~~~~~~~~~~-~~~~PGI~F~Yd~SPi~v~~~~~r~s~~~flt~lcaIiG 212 (222)
T PF07970_consen 134 YMYQYFLKVVPTTYEDLDGFSIETYQYSVTEHSRPLNGGS-SGGLPGIFFKYDFSPIMVVITEDRKSFLHFLTRLCAIIG 212 (222)
T ss_pred eeEEEEEEEeeeeeEeccccccccccccceeeeeeccCCC-CCCCceEEEEEeceeEEEEEEEecCCHHHHHHHHHHHhc
Confidence 4799999999999998864 47999999999999987642 479999999999999999999999999999999999999
Q ss_pred ceeehhhhhH
Q psy1573 80 GVYIVTGTCS 89 (104)
Q Consensus 80 Gvf~v~g~id 89 (104)
|+||++|++|
T Consensus 213 Gvftv~gliD 222 (222)
T PF07970_consen 213 GVFTVAGLID 222 (222)
T ss_pred hHheEEEecC
Confidence 9999999998
No 3
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=60.97 E-value=2.1 Score=24.09 Aligned_cols=31 Identities=23% Similarity=0.207 Sum_probs=23.9
Q ss_pred EeeeccHHHHHHHHHhhhcceeehhhhhHHH
Q psy1573 61 KETRDSFLNFFIRLSGVLGGVYIVTGTCSIS 91 (104)
Q Consensus 61 ~~~~~s~~~flt~lcaIiGGvf~v~g~id~~ 91 (104)
..+|+.|+...+...|-+|++.+..-+++++
T Consensus 8 ~~~RRdFL~~at~~~gavG~~~~a~Pfv~s~ 38 (41)
T PF10399_consen 8 DPTRRDFLTIATSAVGAVGAAAAAWPFVSSM 38 (41)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567889989999999999888877777653
No 4
>KOG4085|consensus
Probab=57.74 E-value=9.3 Score=27.48 Aligned_cols=25 Identities=28% Similarity=0.539 Sum_probs=19.1
Q ss_pred cHHHHHHHHHhhhcceee-hhhhhHH
Q psy1573 66 SFLNFFIRLSGVLGGVYI-VTGTCSI 90 (104)
Q Consensus 66 s~~~flt~lcaIiGGvf~-v~g~id~ 90 (104)
=|+.++.|+.||+||++. ++|.++-
T Consensus 26 Ww~r~l~rl~gilgaf~~~~fGvf~~ 51 (175)
T KOG4085|consen 26 WWYRWLCRLSGILGAFSCAIFGVFNC 51 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 358999999999999987 4444433
No 5
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=53.92 E-value=22 Score=24.37 Aligned_cols=37 Identities=16% Similarity=0.168 Sum_probs=30.3
Q ss_pred eccHHHHHHHHHhhhc-ceeehhhhhHHHHHHHHHHHh
Q psy1573 64 RDSFLNFFIRLSGVLG-GVYIVTGTCSISQGALVEYFR 100 (104)
Q Consensus 64 ~~s~~~flt~lcaIiG-Gvf~v~g~id~~~~~~~~~~~ 100 (104)
+..+..=|.++..+|| +=.+++|+||.++..=++..+
T Consensus 86 ~~e~h~~l~~Iv~~ig~~~~si~~yidNIL~~Hle~~~ 123 (136)
T PF11888_consen 86 SRETHERLSRIVRVIGERKMSISGYIDNILRHHLEEYR 123 (136)
T ss_pred CHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHHH
Confidence 4677888999999999 669999999999987655443
No 6
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=51.83 E-value=8.5 Score=26.46 Aligned_cols=17 Identities=6% Similarity=0.006 Sum_probs=6.8
Q ss_pred hhhhHHHHHHHHHHHhh
Q psy1573 85 TGTCSISQGALVEYFRA 101 (104)
Q Consensus 85 ~g~id~~~~~~~~~~~k 101 (104)
.|+|--+.+...|..||
T Consensus 78 Ig~Illi~y~irR~~Kk 94 (122)
T PF01102_consen 78 IGIILLISYCIRRLRKK 94 (122)
T ss_dssp HHHHHHHHHHHHHHS--
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 34443344444455554
No 7
>PF05365 UCR_UQCRX_QCR9: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like; InterPro: IPR008027 The UQCRX/QCR9 protein is the 9/10 subunit of complex III, and is a protein of about 7 kDa. Deletion of QCR9 results in the inability of Saccharomyces cerevisiae to grow on a fermentable carbon source []. The protein is part of the mitchondrial respiratory chain. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006122 mitochondrial electron transport, ubiquinol to cytochrome c, 0005740 mitochondrial envelope; PDB: 3CX5_T 2IBZ_I 1KYO_I 3CXH_T 1EZV_I 1P84_I 1KB9_I 3H1L_W 3L71_W 3L73_W ....
Probab=44.01 E-value=18 Score=21.51 Aligned_cols=30 Identities=3% Similarity=0.166 Sum_probs=24.4
Q ss_pred HHHHhhhcceeehhhhhHHHHHHHHHHHhh
Q psy1573 72 IRLSGVLGGVYIVTGTCSISQGALVEYFRA 101 (104)
Q Consensus 72 t~lcaIiGGvf~v~g~id~~~~~~~~~~~k 101 (104)
+=+.+|++|.|+.-..+|......-+...|
T Consensus 14 ~y~~~i~~gaf~fe~~fd~~~d~~w~~~Nk 43 (55)
T PF05365_consen 14 TYVLTIFAGAFFFERAFDSATDKIWDSINK 43 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHhccC
Confidence 346789999999999999999988776643
No 8
>TIGR03786 strep_pil_rpt streptococcal pilin isopeptide linkage domain. This model describes a domain that occurs once in the major pilin of Streptococcus pyogenes, Spy0128, but in higher copy numbers in other streptococcal proteins. The domain occurs nine times in a surface-anchored protein of Bifidobacterium longum. All members of this family have LPXTG-type sortase target sequences. The S. pyogenes major pilin has been shown to undergo isopeptide bond cross-linking, mediated by sortases, that are critical to maintaining pilus structural integrity. One such Lys-to-Asn isopeptide bond is to a near-invariant Asn near the C-terminal end of this domain (column 81 of the seed alignment). A Glu in the S. pyogenes major pilin (column 25 of the seed alignment), invariant as Glu or Gln, is described as catalytic for isopeptide bond formation.
Probab=40.92 E-value=81 Score=18.98 Aligned_cols=31 Identities=32% Similarity=0.485 Sum_probs=21.1
Q ss_pred EEeeeEEEEEEEeecCCCCCCceeEEEEEeccceEEEEEeee
Q psy1573 23 TYQYSAKELSRVIDHDVGSHGMSGIFFKYNTNALKVIVKETR 64 (104)
Q Consensus 23 t~QYSvt~~~~~~~~~~~~~~~PGIfF~Yd~sPi~v~~~~~~ 64 (104)
+|.|.+.|.. ...|| +.||=+...|.++-..
T Consensus 11 ~Y~YtV~E~~---------g~~~g--vtYD~~~~~vtV~V~~ 41 (64)
T TIGR03786 11 TYTYTITEVK---------GKEPG--VTYDTTVHTVTVTVTD 41 (64)
T ss_pred EEEEEEEEeC---------CCCCC--eEecCCEEEEEEEEEE
Confidence 7888777763 34567 6899888666665443
No 9
>PF00673 Ribosomal_L5_C: ribosomal L5P family C-terminus; InterPro: IPR002132 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 L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 2ZJR_D 2ZJP_D 3PIO_D 3CF5_D 2ZJQ_D 3DLL_D 3PIP_D 2WDL_G 3UZN_G ....
Probab=37.42 E-value=40 Score=21.78 Aligned_cols=23 Identities=13% Similarity=0.213 Sum_probs=21.7
Q ss_pred ceEEEEEeeeccHHHHHHHHHhh
Q psy1573 55 ALKVIVKETRDSFLNFFIRLSGV 77 (104)
Q Consensus 55 Pi~v~~~~~~~s~~~flt~lcaI 77 (104)
|+.++++-+....+.||-+++.+
T Consensus 1 PiG~kvTLRg~~m~~FL~kli~~ 23 (95)
T PF00673_consen 1 PIGCKVTLRGKKMYEFLDKLITI 23 (95)
T ss_dssp EEEEEEEEEHHHHHHHHHHHHHT
T ss_pred CeEEEEEEccHHHHHHHHHHHHH
Confidence 89999999999999999999887
No 10
>PF11118 DUF2627: Protein of unknown function (DUF2627); InterPro: IPR020138 This entry represents uncharacterised membrane proteins with no known function.
Probab=36.17 E-value=18 Score=23.05 Aligned_cols=22 Identities=27% Similarity=0.326 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhhcceeehhhhh
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTC 88 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~i 88 (104)
|.+|+..+...++|+.-++|+|
T Consensus 40 wlqfl~G~~lf~~G~~Fi~GfI 61 (77)
T PF11118_consen 40 WLQFLAGLLLFAIGVGFIAGFI 61 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHhHh
Confidence 8999999999999999999886
No 11
>PF07413 Herpes_UL37_2: Betaherpesvirus immediate-early glycoprotein UL37; InterPro: IPR010880 This family consists of several Betaherpesvirus immediate-early glycoprotein UL37 sequences. The human cytomegalovirus (HCMV) UL37 immediate-early regulatory protein is a type I integral membrane N-glycoprotein which traffics through the ER and the Golgi network [].
Probab=34.51 E-value=41 Score=26.26 Aligned_cols=43 Identities=9% Similarity=0.038 Sum_probs=31.1
Q ss_pred EEEEeeeccHHHH---HHHHHhhhcceeehhhhhHHHHHHHHHHHh
Q psy1573 58 VIVKETRDSFLNF---FIRLSGVLGGVYIVTGTCSISQGALVEYFR 100 (104)
Q Consensus 58 v~~~~~~~s~~~f---lt~lcaIiGGvf~v~g~id~~~~~~~~~~~ 100 (104)
..+..+.+.+.+. ++++|++.||.++..+++=-++.+..+.+-
T Consensus 228 ~~~~~~~~~l~~~~~~~~g~~~v~~G~~~lL~LFc~l~~~~Rr~i~ 273 (276)
T PF07413_consen 228 FILRVDYRALGHWLAALIGMFFVASGAFMLLSLFCCLSIWRRRDII 273 (276)
T ss_pred EEEecCCcchhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3444555666655 889999999999999988777766655543
No 12
>KOG2014|consensus
Probab=32.29 E-value=13 Score=29.66 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=8.8
Q ss_pred HHHhhhcceee
Q psy1573 73 RLSGVLGGVYI 83 (104)
Q Consensus 73 ~lcaIiGGvf~ 83 (104)
-.||||||+.+
T Consensus 286 Pv~AvVGGiva 296 (331)
T KOG2014|consen 286 PVCAVVGGILA 296 (331)
T ss_pred chhhhhhhHhH
Confidence 47999999853
No 13
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=29.58 E-value=36 Score=18.88 Aligned_cols=29 Identities=7% Similarity=-0.015 Sum_probs=18.0
Q ss_pred HHHhhhcceeehhhhhHHHHHHHHHHHhh
Q psy1573 73 RLSGVLGGVYIVTGTCSISQGALVEYFRA 101 (104)
Q Consensus 73 ~lcaIiGGvf~v~g~id~~~~~~~~~~~k 101 (104)
++.|||.||.+...++--.+.--.--.||
T Consensus 4 s~IaIIv~V~vg~~iiii~~~~YaCcykk 32 (38)
T PF02439_consen 4 STIAIIVAVVVGMAIIIICMFYYACCYKK 32 (38)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 46788888888777666554443333344
No 14
>PF00996 GDI: GDP dissociation inhibitor; InterPro: IPR018203 Rab proteins constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic [, ]; C-terminal geranylgeranylation is crucial for their membrane association and function. This post-translational modification is catalysed by Rab geranylgeranyl transferase (Rab-GGTase), a multi-subunit enzyme that contains a catalytic heterodimer and an accessory component, termed Rab escort protein (REP)-1 []. REP-1 presents newly- synthesised Rab proteins to the catalytic component, and forms a stable complex with the prenylated proteins following the transfer reaction. The mechanism of REP-1-mediated membrane association of Rab5 is similar to that mediated by Rab GDP dissociation inhibitor (GDI). REP-1 and Rab GDI also share other functional properties, including the ability to inhibit the release of GDP and to remove Rab proteins from membranes. The crystal structure of the bovine alpha-isoform of Rab GDI has been determined to a resolution of 1.81A []. The protein is composed of two main structural units: a large complex multi-sheet domain I, and a smaller alpha-helical domain II. The structural organisation of domain I is closely related to FAD-containing monooxygenases and oxidases []. Conserved regions common to GDI and the choroideraemia gene product, which delivers Rab to catalytic subunits of Rab geranylgeranyltransferase II, are clustered on one face of the domain []. The two most conserved regions form a compact structure at the apex of the molecule; site-directed mutagenesis has shown these regions to play a critical role in the binding of Rab proteins [].; PDB: 1VG9_C 1VG0_A 1LTX_R 3P1W_A 3CPH_H 3CPJ_G 3CPI_H 1UKV_G 2BCG_G 1GND_A ....
Probab=28.76 E-value=46 Score=27.46 Aligned_cols=26 Identities=31% Similarity=0.523 Sum_probs=18.8
Q ss_pred ccHHHHHHHHHhhhcceeehhhhhHH
Q psy1573 65 DSFLNFFIRLSGVLGGVYIVTGTCSI 90 (104)
Q Consensus 65 ~s~~~flt~lcaIiGGvf~v~g~id~ 90 (104)
.-+-|=+-|+||+-||+|..-.-++.
T Consensus 232 GELpQ~FcRl~AV~GG~Y~L~~~i~~ 257 (438)
T PF00996_consen 232 GELPQAFCRLSAVYGGTYMLNRPIDE 257 (438)
T ss_dssp THHHHHHHHHHHHTT-EEESS--EEE
T ss_pred ccHHHHHHHHhhhcCcEEEeCCccce
Confidence 35778899999999999987665554
No 15
>PF05931 AgrD: Staphylococcal AgrD protein; InterPro: IPR009229 This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr [].
Probab=27.89 E-value=32 Score=19.70 Aligned_cols=24 Identities=25% Similarity=0.519 Sum_probs=14.8
Q ss_pred HHHHHHHHH---hhhcceeehhhhhHH
Q psy1573 67 FLNFFIRLS---GVLGGVYIVTGTCSI 90 (104)
Q Consensus 67 ~~~flt~lc---aIiGGvf~v~g~id~ 90 (104)
+..+++.+. |.++|.-+|.++.|-
T Consensus 7 ~~~~~t~~f~~IG~~a~~~~C~~~~DE 33 (45)
T PF05931_consen 7 FFKFFTKIFEFIGNVAGYNPCSGYFDE 33 (45)
T ss_pred HHHHHHHHHHHHHhhhccCccceeccC
Confidence 445555554 455566778888773
No 16
>PRK08156 type III secretion system protein SpaS; Validated
Probab=26.55 E-value=72 Score=25.72 Aligned_cols=30 Identities=3% Similarity=0.072 Sum_probs=25.7
Q ss_pred HHHHHHHHHhhhcceeehhhhhHHHHHHHH
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTCSISQGALV 96 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~id~~~~~~~ 96 (104)
+.+.+..+|..+++++.+.+++|-...+..
T Consensus 174 ~~~~~~~l~~~~~~~~lvia~~D~~~Qr~~ 203 (361)
T PRK08156 174 WRELLVKLVLTFLACALIVLILDFIAEYFL 203 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788999999999999999999887753
No 17
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=26.16 E-value=74 Score=25.31 Aligned_cols=29 Identities=17% Similarity=0.161 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhhcceeehhhhhHHHHHHH
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTCSISQGAL 95 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~id~~~~~~ 95 (104)
+.+.+..+|..+++++.+.+++|-...+.
T Consensus 178 ~~~~~~~l~~~~~~~~~via~~D~~~qr~ 206 (342)
T TIGR01404 178 VGELLKLLILVCLGFFLVVGLADFAFQRY 206 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56888899999999999999999988764
No 18
>COG3817 Predicted membrane protein [Function unknown]
Probab=25.40 E-value=47 Score=26.16 Aligned_cols=36 Identities=17% Similarity=0.314 Sum_probs=30.4
Q ss_pred eccHHHHHHHHHhhhcceeehhhhhHHHHHHHHHHH
Q psy1573 64 RDSFLNFFIRLSGVLGGVYIVTGTCSISQGALVEYF 99 (104)
Q Consensus 64 ~~s~~~flt~lcaIiGGvf~v~g~id~~~~~~~~~~ 99 (104)
+.+|.-.+-++.|-+|-+|+.+|.=|.+-+-..+.+
T Consensus 163 ~v~wa~iLPQ~LaaLG~vFa~aGvG~~ia~L~~~~i 198 (313)
T COG3817 163 QVSWAAILPQMLAALGAVFASAGVGDVIAHLISEII 198 (313)
T ss_pred HhhHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHc
Confidence 468999999999999999999999888777665543
No 19
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=24.87 E-value=77 Score=23.30 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=23.4
Q ss_pred cceEEEEEeeeccHHHHHHHHHhhh
Q psy1573 54 NALKVIVKETRDSFLNFFIRLSGVL 78 (104)
Q Consensus 54 sPi~v~~~~~~~s~~~flt~lcaIi 78 (104)
.||.+++|-+....+.||-+++.|.
T Consensus 83 ~pIG~KVTLRg~rm~eFL~rl~~i~ 107 (180)
T COG0094 83 MPIGVKVTLRGERMYEFLDRLLNIA 107 (180)
T ss_pred CeeeEEEEEchHHHHHHHHHHHHhh
Confidence 5899999999999999999999886
No 20
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=23.84 E-value=34 Score=24.04 Aligned_cols=13 Identities=8% Similarity=0.146 Sum_probs=5.6
Q ss_pred eeehhhhhHHHHH
Q psy1573 81 VYIVTGTCSISQG 93 (104)
Q Consensus 81 vf~v~g~id~~~~ 93 (104)
+.++++.|-..++
T Consensus 129 ll~i~~giy~~~r 141 (145)
T PF10661_consen 129 LLAICGGIYVVLR 141 (145)
T ss_pred HHHHHHHHHHHHH
Confidence 3444444444444
No 21
>PRK09108 type III secretion system protein HrcU; Validated
Probab=23.74 E-value=87 Score=25.07 Aligned_cols=30 Identities=17% Similarity=0.423 Sum_probs=25.7
Q ss_pred HHHHHHHHHhhhcceeehhhhhHHHHHHHH
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTCSISQGALV 96 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~id~~~~~~~ 96 (104)
+.+++..++..+++++.+.+++|-...+..
T Consensus 181 ~~~~~~~l~~~~~~~~~via~~D~~~qr~~ 210 (353)
T PRK09108 181 LWTVLMKLLAVAAGVFLLVGAADWKIQRWL 210 (353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888999999999999999999887653
No 22
>COG5056 ARE1 Acyl-CoA cholesterol acyltransferase [Lipid metabolism]
Probab=23.71 E-value=74 Score=26.76 Aligned_cols=33 Identities=6% Similarity=0.137 Sum_probs=28.3
Q ss_pred eeccHHHHHHHHHhhhcceeehhhhhHHHHHHH
Q psy1573 63 TRDSFLNFFIRLSGVLGGVYIVTGTCSISQGAL 95 (104)
Q Consensus 63 ~~~s~~~flt~lcaIiGGvf~v~g~id~~~~~~ 95 (104)
.|..|.-.+-..||++|++|-.+-..|..+.-+
T Consensus 298 a~~rw~yvleK~~~~fg~ifL~vi~~d~ymvPv 330 (512)
T COG5056 298 ARIRWRYVLEKACATFGTIFLMVIVADQYMVPV 330 (512)
T ss_pred heeeHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 457888999999999999999999999877653
No 23
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=23.70 E-value=88 Score=25.01 Aligned_cols=30 Identities=23% Similarity=0.195 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhhcceeehhhhhHHHHHHHH
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTCSISQGALV 96 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~id~~~~~~~ 96 (104)
+.+.+..++..+.+++.+.+++|-+..+..
T Consensus 179 ~~~~~~~l~~~~~~~~~via~~D~~~qr~~ 208 (349)
T PRK12721 179 VSTLIFWLWGGLLACYLVFGILDYSFQRYK 208 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568888999999999999999998887653
No 24
>smart00794 AgrD Staphylococcal AgrD protein. This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons con
Probab=23.51 E-value=44 Score=19.15 Aligned_cols=20 Identities=25% Similarity=0.283 Sum_probs=13.6
Q ss_pred HHHHHhhhcceeehhhhhHH
Q psy1573 71 FIRLSGVLGGVYIVTGTCSI 90 (104)
Q Consensus 71 lt~lcaIiGGvf~v~g~id~ 90 (104)
+-...|.++|.-+|.++.|-
T Consensus 14 ~f~~IG~~a~~~~C~~~fDE 33 (45)
T smart00794 14 FFESIGNVAGYNPCTGYFDE 33 (45)
T ss_pred HHHHHHHHhcCCcccccCCC
Confidence 33445666677889988873
No 25
>PRK00010 rplE 50S ribosomal protein L5; Validated
Probab=23.40 E-value=94 Score=22.55 Aligned_cols=25 Identities=16% Similarity=0.223 Sum_probs=23.0
Q ss_pred cceEEEEEeeeccHHHHHHHHHhhh
Q psy1573 54 NALKVIVKETRDSFLNFFIRLSGVL 78 (104)
Q Consensus 54 sPi~v~~~~~~~s~~~flt~lcaIi 78 (104)
.|+.++++-+....++||-+++.++
T Consensus 83 ~piG~kVTLRg~~my~FL~kli~~v 107 (179)
T PRK00010 83 MPIGCKVTLRGERMYEFLDRLINIA 107 (179)
T ss_pred CEEEEEEEECcHHHHHHHHHHHHHh
Confidence 5799999999999999999999876
No 26
>COG3765 WzzB Chain length determinant protein [Cell envelope biogenesis, outer membrane]
Probab=23.24 E-value=55 Score=26.44 Aligned_cols=40 Identities=10% Similarity=0.190 Sum_probs=28.5
Q ss_pred EEEEeccceEEEEEeeeccHHHHHHHHHhhhcceeehhhhhH
Q psy1573 48 FFKYNTNALKVIVKETRDSFLNFFIRLSGVLGGVYIVTGTCS 89 (104)
Q Consensus 48 fF~Yd~sPi~v~~~~~~~s~~~flt~lcaIiGGvf~v~g~id 89 (104)
-|+|+-+|-.=.... .|=..+++-+.|+|||++.+...+=
T Consensus 298 ~yRYl~~P~~Pvkrd--~PrrA~ilil~~LiGgm~g~g~vL~ 337 (347)
T COG3765 298 TYRYLQKPTLPVKRD--SPRRAIILILGALIGGMLGAGVVLL 337 (347)
T ss_pred EEEecCCCCCCCcCC--CcchHHHHHHHHHHHHHHHHHHHHH
Confidence 478888886544332 3446788899999999988776543
No 27
>KOG1652|consensus
Probab=23.00 E-value=57 Score=24.05 Aligned_cols=28 Identities=21% Similarity=0.183 Sum_probs=23.4
Q ss_pred hhhcceeehhhhhHHHHHHHHHHHhhhc
Q psy1573 76 GVLGGVYIVTGTCSISQGALVEYFRAME 103 (104)
Q Consensus 76 aIiGGvf~v~g~id~~~~~~~~~~~k~~ 103 (104)
.-+||-|++-|-+.+.++-++..+||.|
T Consensus 58 p~~ggsFAvwgglfSt~dC~Lv~~R~Ke 85 (183)
T KOG1652|consen 58 PQSGGSFAVWGGLFSTVDCALVAIRKKE 85 (183)
T ss_pred cccccceeeeechhhHHHHHHHHHhccc
Confidence 5679999999999999988888887655
No 28
>PF09881 DUF2108: Predicted membrane protein (DUF2108); InterPro: IPR019213 This entry is found in various hypothetical archaeal proteins, has no known function.
Probab=22.76 E-value=65 Score=20.26 Aligned_cols=19 Identities=11% Similarity=0.329 Sum_probs=14.5
Q ss_pred cHHHHHHHHHhhhcceeeh
Q psy1573 66 SFLNFFIRLSGVLGGVYIV 84 (104)
Q Consensus 66 s~~~flt~lcaIiGGvf~v 84 (104)
.+...+.-.||++||+-++
T Consensus 2 ~~l~li~~~~~iiG~ig~i 20 (72)
T PF09881_consen 2 EILPLISAACAIIGAIGAI 20 (72)
T ss_pred ccHHHHHHHHHHHhhheee
Confidence 3456777889999998765
No 29
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=22.62 E-value=94 Score=25.25 Aligned_cols=30 Identities=10% Similarity=-0.208 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhhcceeehhhhhHHHHHHHH
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTCSISQGALV 96 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~id~~~~~~~ 96 (104)
+.+++..++..++.++.+.+++|-+..+..
T Consensus 186 ~~~~~~~l~~~~~~~~~via~~D~~~qr~~ 215 (386)
T PRK12468 186 ALHLIIFCGLVVVLGLSPMVGFDVFYQITS 215 (386)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888899999999999999999887653
No 30
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=22.07 E-value=51 Score=25.59 Aligned_cols=15 Identities=20% Similarity=0.386 Sum_probs=11.1
Q ss_pred ccHHHHHHHHHhhhc
Q psy1573 65 DSFLNFFIRLSGVLG 79 (104)
Q Consensus 65 ~s~~~flt~lcaIiG 79 (104)
-++.|.|+++|.|||
T Consensus 250 lAvlHtiiSf~clIg 264 (274)
T PF06459_consen 250 LAVLHTIISFACLIG 264 (274)
T ss_pred HHHHHHHHHHHHHHH
Confidence 346788888888876
No 31
>PF11688 DUF3285: Protein of unknown function (DUF3285); InterPro: IPR021702 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=22.02 E-value=35 Score=19.53 Aligned_cols=21 Identities=24% Similarity=0.430 Sum_probs=16.0
Q ss_pred EeeeccHHHHHHHHHhhhcce
Q psy1573 61 KETRDSFLNFFIRLSGVLGGV 81 (104)
Q Consensus 61 ~~~~~s~~~flt~lcaIiGGv 81 (104)
+..++|+.||.....|.+|=+
T Consensus 17 RKg~~SL~HF~LT~~gll~~l 37 (45)
T PF11688_consen 17 RKGGTSLFHFGLTAVGLLGFL 37 (45)
T ss_pred HccCcchhHHHHHHHHHHHHH
Confidence 345689999999888887643
No 32
>PF15103 G0-G1_switch_2: G0/G1 switch protein 2
Probab=21.40 E-value=33 Score=22.98 Aligned_cols=23 Identities=26% Similarity=0.252 Sum_probs=18.4
Q ss_pred hhcceeehhhhhHHHHHHHHHHH
Q psy1573 77 VLGGVYIVTGTCSISQGALVEYF 99 (104)
Q Consensus 77 IiGGvf~v~g~id~~~~~~~~~~ 99 (104)
++|+++++.|++-.++..+...|
T Consensus 28 vLGSvLA~~Gvv~GLVEtVCsPF 50 (102)
T PF15103_consen 28 VLGSVLAFFGVVIGLVETVCSPF 50 (102)
T ss_pred hhhhHHHHHHHHHHHHHHHhCcc
Confidence 67999999999888888776544
No 33
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=21.40 E-value=1e+02 Score=24.58 Aligned_cols=29 Identities=14% Similarity=0.014 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhhcceeehhhhhHHHHHHH
Q psy1573 67 FLNFFIRLSGVLGGVYIVTGTCSISQGAL 95 (104)
Q Consensus 67 ~~~flt~lcaIiGGvf~v~g~id~~~~~~ 95 (104)
+.+.+..++..+++++.+.+++|-...+.
T Consensus 179 ~~~~~~~l~~~~~~~~~via~~D~~~qr~ 207 (347)
T TIGR00328 179 FLDIAKSLLILVLLLLLVIAVFDYFFQRW 207 (347)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788899999999999999999887764
No 34
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.30 E-value=1.2e+02 Score=17.26 Aligned_cols=17 Identities=6% Similarity=0.036 Sum_probs=11.4
Q ss_pred hhhHHHHHHHHHHHhhh
Q psy1573 86 GTCSISQGALVEYFRAM 102 (104)
Q Consensus 86 g~id~~~~~~~~~~~k~ 102 (104)
+++|++..++..-|||+
T Consensus 19 SLLdrItRklr~gwKRl 35 (45)
T PF02061_consen 19 SLLDRITRKLRDGWKRL 35 (45)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 56677777776667653
No 35
>PRK04219 rpl5p 50S ribosomal protein L5P; Reviewed
Probab=20.54 E-value=1.1e+02 Score=22.26 Aligned_cols=25 Identities=12% Similarity=0.093 Sum_probs=23.3
Q ss_pred cceEEEEEeeeccHHHHHHHHHhhh
Q psy1573 54 NALKVIVKETRDSFLNFFIRLSGVL 78 (104)
Q Consensus 54 sPi~v~~~~~~~s~~~flt~lcaIi 78 (104)
.|+.++++-+....++||-+|+.++
T Consensus 66 ~pIG~kVTLRg~~m~~FL~rli~iv 90 (177)
T PRK04219 66 EPIGVKVTLRGEKAEEFLKTALEAV 90 (177)
T ss_pred CEEEEEEEEccHHHHHHHHHHHHhh
Confidence 5999999999999999999999986
No 36
>KOG4405|consensus
Probab=20.32 E-value=53 Score=27.70 Aligned_cols=27 Identities=26% Similarity=0.517 Sum_probs=20.9
Q ss_pred ccHHHHHHHHHhhhcceeehhhhhHHH
Q psy1573 65 DSFLNFFIRLSGVLGGVYIVTGTCSIS 91 (104)
Q Consensus 65 ~s~~~flt~lcaIiGGvf~v~g~id~~ 91 (104)
.-+-|=+-|+||+.||++..-.-++.+
T Consensus 286 GELpQcFCRlcAVfGgIYcLr~~Vq~i 312 (547)
T KOG4405|consen 286 GELPQCFCRLCAVFGGIYCLRRPVQAI 312 (547)
T ss_pred CcchHHHHHHHHHhcceEEeccchhhe
Confidence 456688889999999999876555543
No 37
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=20.17 E-value=64 Score=20.85 Aligned_cols=37 Identities=14% Similarity=0.207 Sum_probs=27.5
Q ss_pred EEeeeccHHHHHHHHHhhhcceeehhhhhHHHHHHHHHH
Q psy1573 60 VKETRDSFLNFFIRLSGVLGGVYIVTGTCSISQGALVEY 98 (104)
Q Consensus 60 ~~~~~~s~~~flt~lcaIiGGvf~v~g~id~~~~~~~~~ 98 (104)
+++.+.=+-+|+.=+||++ +|.+.-++--++......
T Consensus 26 VsrN~sfirdFvLVic~~l--VfVii~lFi~ll~~i~~~ 62 (84)
T PF06143_consen 26 VSRNRSFIRDFVLVICCFL--VFVIIVLFILLLYNINKN 62 (84)
T ss_pred HHhChHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 3556666789999999997 888777777777665543
Done!