Query 033297
Match_columns 122
No_of_seqs 102 out of 189
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 12:11:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033297.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033297hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02290 SRP14: Signal recogni 100.0 2.5E-41 5.4E-46 236.0 8.3 90 4-93 1-93 (93)
2 KOG1761 Signal recognition par 100.0 8.8E-39 1.9E-43 230.5 9.9 105 2-106 1-108 (116)
3 PF03791 KNOX2: KNOX2 domain ; 73.4 2.9 6.4E-05 26.5 2.0 18 71-88 7-24 (52)
4 KOG3465 Signal recognition par 58.2 15 0.00032 25.7 3.2 29 1-31 1-30 (86)
5 PF02786 CPSase_L_D2: Carbamoy 44.1 35 0.00076 26.5 3.8 34 52-85 38-73 (211)
6 PF08482 HrpB_C: ATP-dependent 39.1 18 0.00039 26.9 1.4 17 72-88 102-119 (133)
7 KOG1572 Predicted protein tyro 36.9 13 0.00028 30.5 0.3 22 50-71 146-167 (249)
8 PF03418 Peptidase_A25: Germin 30.3 50 0.0011 28.5 2.8 29 66-94 312-341 (354)
9 KOG3442 Uncharacterized conser 30.0 57 0.0012 24.4 2.7 30 3-32 70-101 (132)
10 PF12108 SF3a60_bindingd: Spli 24.5 69 0.0015 17.8 1.8 17 69-85 3-19 (28)
11 COG5453 Uncharacterized conser 23.6 60 0.0013 23.0 1.8 13 49-61 24-37 (96)
12 PF14775 NYD-SP28_assoc: Sperm 22.7 68 0.0015 20.5 1.8 18 74-91 20-37 (60)
13 PF08293 MRP-S33: Mitochondria 22.1 39 0.00085 23.0 0.6 11 108-118 77-87 (87)
14 PRK01683 trans-aconitate 2-met 21.2 86 0.0019 24.1 2.4 28 7-34 221-251 (258)
15 smart00555 GIT Helical motif i 20.4 97 0.0021 17.4 1.9 17 3-19 7-23 (31)
No 1
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 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 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=100.00 E-value=2.5e-41 Score=236.04 Aligned_cols=90 Identities=50% Similarity=0.753 Sum_probs=68.0
Q ss_pred CCchHHHHHHHHHHhhcCCCc-eEEEEEecCCCCCcccccccC-CCCCCCceeeEEEEeCCCc-eEEEEeccccHHHHHH
Q 033297 4 LQPDPFLNELTSMFERNRDKG-SVWVTFKRSSMKSKSQKNKMA-TAGEPVEYRCLIRATDGKQ-KISTTVGAKDHQRFQA 80 (122)
Q Consensus 4 L~ndeFL~~L~~Lf~~~~~~g-SV~lT~KR~~~~~~~~~~~~~-~~~~~~ey~~LiRAt~Gk~-KiSTvV~~~~l~~F~~ 80 (122)
||||+||++|++||+.++++| |||||||||++.+.+.+.... ...++.||+||||||||++ ||||+|+++||++||+
T Consensus 1 L~ndeFL~~L~~lf~~~~~k~gSV~lT~KR~~~~~k~~~~~~~~~~~~~~~~~~LiRAt~Gkk~KiSTvV~~~~l~~F~~ 80 (93)
T PF02290_consen 1 LSNDEFLSELTKLFEKSKEKGGSVYLTQKRLDGKTKPKPKKQKPSSSEDKEYPCLIRATNGKKIKISTVVDPDDLDKFWQ 80 (93)
T ss_dssp E-HHHHHHHHHHHHHHCSSSSS-EEEEEEEEEE-------------------EEEEEEESSSS-EEEEEEETTCHHHHHH
T ss_pred CCHHHHHHHHHHHHHHcccCCceEEEEEeecCCCCCCCCccccCCCCCCCCceEEEEEecCCCCeEEEEECHHHHHHHHH
Confidence 799999999999999999876 999999999887655444332 3345679999999999998 9999999999999999
Q ss_pred HHHHHHHhhcccc
Q 033297 81 SYATLLKAHMAAL 93 (122)
Q Consensus 81 ~Y~~vlK~~M~~L 93 (122)
+|++|||+||+||
T Consensus 81 ~Y~~v~K~~M~~L 93 (93)
T PF02290_consen 81 SYANVLKAGMDGL 93 (93)
T ss_dssp HHHHHHHHHCCTS
T ss_pred HHHHHHHhhCcCC
Confidence 9999999999998
No 2
>KOG1761 consensus Signal recognition particle, subunit Srp14 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8.8e-39 Score=230.48 Aligned_cols=105 Identities=51% Similarity=0.796 Sum_probs=96.8
Q ss_pred CCCCchHHHHHHHHHHhhcCCCc--eEEEEEecCCCCCcccccccCCCC-CCCceeeEEEEeCCCceEEEEeccccHHHH
Q 033297 2 GLLQPDPFLNELTSMFERNRDKG--SVWVTFKRSSMKSKSQKNKMATAG-EPVEYRCLIRATDGKQKISTTVGAKDHQRF 78 (122)
Q Consensus 2 vlL~ndeFL~~L~~Lf~~~~~~g--SV~lT~KR~~~~~~~~~~~~~~~~-~~~ey~~LiRAt~Gk~KiSTvV~~~~l~~F 78 (122)
++|++++||++|+.||+.++..| |||||+|||++.+++.+.....+. ++.+|+|||||++|++||||||.++|+++|
T Consensus 1 ~~~~~~~Fl~~lt~~~q~~k~~g~~sv~it~k~~dgrtk~~p~kgs~~g~e~~e~~cLiRa~~G~kKiSTVV~akev~~F 80 (116)
T KOG1761|consen 1 MLLESEQFLTELTRLFQKSKIKGASSVYITLKRYDGRTKPVPKKGSVEGFEPSEYRCLIRATDGKKKISTVVKAKEVNKF 80 (116)
T ss_pred CCccchHHHHHHHHHHHhhhhcCCcceEEEEeccCCCcccccccCCcCCCCCccceEEEEeccCCceEEEEEeHHHHHHH
Confidence 57899999999999999999888 999999999999998888777665 788999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccccccccccccCCc
Q 033297 79 QASYATLLKAHMAALKKRERKDKKKGVD 106 (122)
Q Consensus 79 ~~~Y~~vlK~~M~~LkKrdKkk~K~k~~ 106 (122)
|++|++||+++|+||+||+|++.++++.
T Consensus 81 ~~~YS~vlk~~M~~LkKr~kk~~kkk~~ 108 (116)
T KOG1761|consen 81 QQSYSAVLKAQMDGLKKRKKKKSKKKTK 108 (116)
T ss_pred HHHHHHHHHHHhhhhhhcccccccccce
Confidence 9999999999999999999988765443
No 3
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=73.41 E-value=2.9 Score=26.51 Aligned_cols=18 Identities=17% Similarity=0.425 Sum_probs=15.0
Q ss_pred ccccHHHHHHHHHHHHHh
Q 033297 71 GAKDHQRFQASYATLLKA 88 (122)
Q Consensus 71 ~~~~l~~F~~~Y~~vlK~ 88 (122)
.-.+||.|..+|..+|..
T Consensus 7 ~dpELDqFMeaYc~~L~k 24 (52)
T PF03791_consen 7 ADPELDQFMEAYCDMLVK 24 (52)
T ss_pred CCccHHHHHHHHHHHHHH
Confidence 345899999999999864
No 4
>KOG3465 consensus Signal recognition particle, subunit Srp9 [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.20 E-value=15 Score=25.66 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=24.6
Q ss_pred CCCCCc-hHHHHHHHHHHhhcCCCceEEEEEe
Q 033297 1 MGLLQP-DPFLNELTSMFERNRDKGSVWVTFK 31 (122)
Q Consensus 1 MvlL~n-deFL~~L~~Lf~~~~~~gSV~lT~K 31 (122)
||.+.+ |||+..-..||..+.+ +..++||
T Consensus 1 Mvy~qtwdEF~~ase~L~~A~P~--~~RlvmK 30 (86)
T KOG3465|consen 1 MVYLQTWDEFFTASESLYLANPE--KTRLVMK 30 (86)
T ss_pred CceeeeHHHHHHHHHHHHhcCcc--ceEEEEE
Confidence 777776 9999999999998765 5788888
No 5
>PF02786 CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain; InterPro: IPR005479 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the ATP-binding domain found in the large subunit of carbamoyl phosphate synthase, as well as in related proteins.; GO: 0003824 catalytic activity, 0005524 ATP binding, 0008152 metabolic process; PDB: 3U9S_A 3U9T_A 2C00_B 2VQD_A 1W96_B 1W93_A 1M6V_C 1CS0_C 1C30_E 1C3O_G ....
Probab=44.15 E-value=35 Score=26.55 Aligned_cols=34 Identities=15% Similarity=0.198 Sum_probs=20.8
Q ss_pred ceeeEEEEeCCC--ceEEEEeccccHHHHHHHHHHH
Q 033297 52 EYRCLIRATDGK--QKISTTVGAKDHQRFQASYATL 85 (122)
Q Consensus 52 ey~~LiRAt~Gk--~KiSTvV~~~~l~~F~~~Y~~v 85 (122)
.||||||++.|- +-+--+=+.++|....+.-...
T Consensus 38 GyPVliKas~ggGG~gm~iv~~~~eL~~~~~~~~~~ 73 (211)
T PF02786_consen 38 GYPVLIKASAGGGGRGMRIVHNEEELEEAFERAQRE 73 (211)
T ss_dssp -SSEEEEETTSSTTTSEEEESSHHHHHHHHHHHHHH
T ss_pred CCceEEeecccccccccccccchhhhhhhhhhcccc
Confidence 599999999863 3444444556666665544333
No 6
>PF08482 HrpB_C: ATP-dependent helicase C-terminal; InterPro: IPR013689 This domain is found near the C terminus of bacterial ATP-dependent helicases such as HrpB.
Probab=39.10 E-value=18 Score=26.93 Aligned_cols=17 Identities=29% Similarity=0.425 Sum_probs=14.3
Q ss_pred cccHHHHHH-HHHHHHHh
Q 033297 72 AKDHQRFQA-SYATLLKA 88 (122)
Q Consensus 72 ~~~l~~F~~-~Y~~vlK~ 88 (122)
..||..||+ .|.+|-|-
T Consensus 102 T~DL~~FW~~sY~~VrKe 119 (133)
T PF08482_consen 102 TQDLASFWQGSYPEVRKE 119 (133)
T ss_pred eCCHHHHhcccHHHHHHH
Confidence 489999999 89988763
No 7
>KOG1572 consensus Predicted protein tyrosine phosphatase [Defense mechanisms]
Probab=36.92 E-value=13 Score=30.52 Aligned_cols=22 Identities=32% Similarity=0.527 Sum_probs=19.1
Q ss_pred CCceeeEEEEeCCCceEEEEec
Q 033297 50 PVEYRCLIRATDGKQKISTTVG 71 (122)
Q Consensus 50 ~~ey~~LiRAt~Gk~KiSTvV~ 71 (122)
...|||||+.+.|+..+.|+|-
T Consensus 146 ~~N~P~Lihc~rGkhRtg~lVg 167 (249)
T KOG1572|consen 146 KRNYPILIHCKRGKHRTGCLVG 167 (249)
T ss_pred ccCCceEEecCCCCcchhhhHH
Confidence 4579999999999999988883
No 8
>PF03418 Peptidase_A25: Germination protease This family belongs to family A25 of the peptidase classification.; InterPro: IPR005080 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date []. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family A25 (gpr protease family, clan AE). These are tetrameric proteases that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species during spore germination. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0009847 spore germination; PDB: 1C8B_A.
Probab=30.28 E-value=50 Score=28.46 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.6
Q ss_pred EEEEeccccHHHHHHHHHHHHHhhcc-ccc
Q 033297 66 ISTTVGAKDHQRFQASYATLLKAHMA-ALK 94 (122)
Q Consensus 66 iSTvV~~~~l~~F~~~Y~~vlK~~M~-~Lk 94 (122)
-+-+|+|+|+|.|..+++.++=.|++ +|-
T Consensus 312 ~~L~VTPKEID~~Ie~~a~iIA~GiN~ALh 341 (354)
T PF03418_consen 312 GNLMVTPKEIDELIEDLAKIIANGINMALH 341 (354)
T ss_dssp TTEEEEETTHHHHHHHHHHHHHHHHGGGGS
T ss_pred CCceECcHhHHHHHHHHHHHHHHHHHHHhC
Confidence 46799999999999999999999988 454
No 9
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.98 E-value=57 Score=24.43 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=24.4
Q ss_pred CCCchHHHHHHHHHHhhcCC--CceEEEEEec
Q 033297 3 LLQPDPFLNELTSMFERNRD--KGSVWVTFKR 32 (122)
Q Consensus 3 lL~ndeFL~~L~~Lf~~~~~--~gSV~lT~KR 32 (122)
.|+.|+-...-..||+-+.. .||.||--|=
T Consensus 70 ~ln~eei~k~yehLFevNdkskGGSFYLQSKV 101 (132)
T KOG3442|consen 70 PLNREEIEKRYEHLFEVNDKSKGGSFYLQSKV 101 (132)
T ss_pred CCCHHHHHHHHHHHHhccCcccCcceeehHHH
Confidence 46678899999999999863 4799998774
No 10
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=24.54 E-value=69 Score=17.78 Aligned_cols=17 Identities=12% Similarity=0.260 Sum_probs=11.2
Q ss_pred EeccccHHHHHHHHHHH
Q 033297 69 TVGAKDHQRFQASYATL 85 (122)
Q Consensus 69 vV~~~~l~~F~~~Y~~v 85 (122)
+-.+++...|+.++.+|
T Consensus 3 is~~d~f~eFY~rlk~I 19 (28)
T PF12108_consen 3 ISGGDPFSEFYERLKEI 19 (28)
T ss_dssp --S--HHHHHHHHHHHH
T ss_pred CCCCChHHHHHHHHHHH
Confidence 44678999999998876
No 11
>COG5453 Uncharacterized conserved protein [Function unknown]
Probab=23.58 E-value=60 Score=23.03 Aligned_cols=13 Identities=54% Similarity=0.641 Sum_probs=9.5
Q ss_pred CCCce-eeEEEEeC
Q 033297 49 EPVEY-RCLIRATD 61 (122)
Q Consensus 49 ~~~ey-~~LiRAt~ 61 (122)
++.|| .|||+||-
T Consensus 24 ~~~ehkdflI~atP 37 (96)
T COG5453 24 EPIEHKDFLIYATP 37 (96)
T ss_pred CcccccCeEEEeee
Confidence 44566 79999984
No 12
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=22.72 E-value=68 Score=20.50 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=14.4
Q ss_pred cHHHHHHHHHHHHHhhcc
Q 033297 74 DHQRFQASYATLLKAHMA 91 (122)
Q Consensus 74 ~l~~F~~~Y~~vlK~~M~ 91 (122)
.|+.|+..|..||.--..
T Consensus 20 ~L~~~l~rY~~vL~~R~~ 37 (60)
T PF14775_consen 20 ALENFLKRYNKVLLDRAA 37 (60)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 688999999999875443
No 13
>PF08293 MRP-S33: Mitochondrial ribosomal subunit S27; InterPro: IPR013219 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 [, ]. This entry represents a mitochondrial ribosomal subunit annotated as S27 in yeast and S33 in humans [, ]. It is a small 106 residue protein. The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome [].
Probab=22.09 E-value=39 Score=22.98 Aligned_cols=11 Identities=36% Similarity=0.743 Sum_probs=8.0
Q ss_pred CCCCCCCCCCC
Q 033297 108 DRKDGAGSTKK 118 (122)
Q Consensus 108 ~~~~~~~~~~~ 118 (122)
.+.+|+|+|||
T Consensus 77 rk~RGKg~PKK 87 (87)
T PF08293_consen 77 RKRRGKGPPKK 87 (87)
T ss_pred HHhCCCCCCCC
Confidence 45678888876
No 14
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=21.17 E-value=86 Score=24.05 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHhhc---CCCceEEEEEecCC
Q 033297 7 DPFLNELTSMFERN---RDKGSVWVTFKRSS 34 (122)
Q Consensus 7 deFL~~L~~Lf~~~---~~~gSV~lT~KR~~ 34 (122)
++|+.++.+.|... ...|++++++.|+.
T Consensus 221 ~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 251 (258)
T PRK01683 221 AAFLAAYLARIAEAYPLQADGKVLLAFPRLF 251 (258)
T ss_pred HHHHHHHHHHHHHHCCCCCCCcEEcccceEE
Confidence 78999999988765 35788999887753
No 15
>smart00555 GIT Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins. Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins, and in yeast Spa2p and Sph1p (CPP; unpublished results). In p95-APP1 the N-terminal GIT motif might be involved in binding PIX.
Probab=20.43 E-value=97 Score=17.38 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=14.9
Q ss_pred CCCchHHHHHHHHHHhh
Q 033297 3 LLQPDPFLNELTSMFER 19 (122)
Q Consensus 3 lL~ndeFL~~L~~Lf~~ 19 (122)
.|++.+|..-++.+|..
T Consensus 7 ~L~~~~F~~L~~Dv~~E 23 (31)
T smart00555 7 RLSDEQFQKLLTDLNDE 23 (31)
T ss_pred hcCHHHHHHHHHHHHHH
Confidence 58899999999999875
Done!