Query 041207
Match_columns 126
No_of_seqs 122 out of 274
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:50:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041207.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041207hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3295 60S Ribosomal protein 100.0 1.7E-53 3.8E-58 335.3 8.0 126 1-126 80-205 (205)
2 PTZ00352 60S ribosomal protein 100.0 1.4E-50 3E-55 322.1 8.7 123 1-123 80-211 (212)
3 PTZ00192 60S ribosomal protein 100.0 7.5E-50 1.6E-54 318.8 8.9 119 1-124 87-214 (218)
4 PF01294 Ribosomal_L13e: Ribos 100.0 5E-45 1.1E-49 284.7 0.2 103 1-103 77-179 (179)
5 PRK12277 50S ribosomal protein 99.8 2.7E-20 6E-25 130.3 2.3 39 1-43 41-79 (83)
6 COG4352 RPL13 Ribosomal protei 99.7 1.5E-17 3.3E-22 121.8 1.8 46 1-46 68-113 (113)
7 PF13318 DUF4089: Protein of u 56.1 3.1 6.8E-05 26.5 -0.4 36 8-47 5-40 (50)
8 PF14265 DUF4355: Domain of un 50.9 6.4 0.00014 28.1 0.5 34 2-43 81-114 (125)
9 smart00563 PlsC Phosphate acyl 34.3 41 0.00089 21.9 2.4 36 13-49 50-85 (118)
10 PLN02510 probable 1-acyl-sn-gl 34.0 43 0.00094 29.0 3.1 37 13-50 145-183 (374)
11 PF11324 DUF3126: Protein of u 32.6 35 0.00076 23.0 1.8 23 32-58 2-30 (63)
12 KOG0304 mRNA deadenylase subun 32.1 26 0.00056 29.2 1.3 46 7-57 36-84 (239)
13 cd07988 LPLAT_ABO13168-like Ly 31.0 94 0.002 23.1 4.1 59 13-76 71-131 (163)
14 cd07573 CPA N-carbamoylputresc 27.2 48 0.001 26.0 2.1 23 26-48 12-41 (284)
15 PRK13286 amiE acylamide amidoh 26.6 60 0.0013 27.5 2.7 25 24-48 27-60 (345)
16 PF10587 EF-1_beta_acid: Eukar 26.4 73 0.0016 18.4 2.2 17 25-41 11-27 (28)
17 cd07576 R-amidase_like Pseudom 26.4 57 0.0012 25.0 2.3 23 26-48 12-41 (254)
18 cd07582 nitrilase_4 Uncharacte 26.2 61 0.0013 26.0 2.6 26 23-48 14-51 (294)
19 cd07570 GAT_Gln-NAD-synth Glut 26.0 56 0.0012 25.3 2.2 23 27-49 13-42 (261)
20 PF00795 CN_hydrolase: Carbon- 24.0 77 0.0017 22.9 2.5 25 24-48 12-43 (186)
21 cd07584 nitrilase_6 Uncharacte 23.7 68 0.0015 24.7 2.3 23 26-48 12-41 (258)
22 PLN02380 1-acyl-sn-glycerol-3- 23.7 73 0.0016 27.7 2.7 36 14-50 138-175 (376)
23 cd07581 nitrilase_3 Uncharacte 23.5 60 0.0013 24.9 2.0 24 26-49 10-40 (255)
24 cd07577 Ph0642_like Pyrococcus 22.9 70 0.0015 24.8 2.2 23 26-48 12-38 (259)
25 KOG3995 3-hydroxyanthranilate 22.7 38 0.00081 28.5 0.7 22 5-26 95-116 (279)
26 cd07574 nitrilase_Rim1_like Un 22.1 71 0.0015 25.0 2.2 24 26-49 14-44 (280)
27 PF00058 Ldl_recept_b: Low-den 22.0 36 0.00078 20.1 0.4 9 10-18 34-42 (42)
28 COG1999 Uncharacterized protei 22.0 73 0.0016 25.0 2.2 28 10-47 106-133 (207)
29 cd07197 nitrilase Nitrilase su 20.5 89 0.0019 23.6 2.3 23 26-48 11-40 (253)
No 1
>KOG3295 consensus 60S Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-53 Score=335.34 Aligned_cols=126 Identities=58% Similarity=0.816 Sum_probs=123.8
Q ss_pred CCCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeecCCccccccCCCCHHHhhhhhhccCccCCCCCCCC
Q 041207 1 AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAGDSAPEELATATQVQGPYMPIAPERP 80 (126)
Q Consensus 1 aAGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPrk~~kpkkGDs~~ee~~~a~q~~~~v~Pi~~~~~ 80 (126)
+|||++++|+||||||||||+|+|+|+||.||||||+|+|||||||+++++|++|||++||+++++|++|++|||.+...
T Consensus 80 ~AGi~k~~A~tiGIaVD~RRrn~s~E~lqaNvqRlKey~sklilfprk~~apkkGdSsaeel~~atq~~g~~mPi~~~~~ 159 (205)
T KOG3295|consen 80 AAGISKKVARTIGIAVDHRRRNRSQEGLQANVQRLKEYKSKLILFPRKASAPKKGDSSAEELKLATQLTGPVMPIVNVYA 159 (205)
T ss_pred HcCccHhhccceeeeecccccCccHHHHHHhHHHHHHhhcceEEeecCcCCCcCCCCcHHHHHhhhhhcCCCcCccccch
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCcccccchHHHHHHHHHhhhhhhhhhhhHHHHHHHhhcC
Q 041207 81 TVELVKVTQDMKSFKAYDKLRIERVNERHFGARMKKAAEAEKEEKK 126 (126)
Q Consensus 81 ~~~~r~it~eek~~~ay~~LR~ar~~~r~~G~r~kra~~~ae~~~~ 126 (126)
.++++.+|+|++.|+||++||++|+|+||.|+|+||++|++|+|+|
T Consensus 160 ~eEa~~~t~e~k~f~Af~~lr~aRa~ar~~g~raKRa~Eaae~EkK 205 (205)
T KOG3295|consen 160 KEEARVVTDEEKNFKAFRTLRLARANARLAGIRAKRAKEAAEEEKK 205 (205)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhHHHHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999999999999865
No 2
>PTZ00352 60S ribosomal protein L13; Provisional
Probab=100.00 E-value=1.4e-50 Score=322.13 Aligned_cols=123 Identities=38% Similarity=0.630 Sum_probs=119.1
Q ss_pred CCCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeecCCccccccC------CCCHHHhhh--hh-hccCc
Q 041207 1 AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAG------DSAPEELAT--AT-QVQGP 71 (126)
Q Consensus 1 aAGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPrk~~kpkkG------Ds~~ee~~~--a~-q~~~~ 71 (126)
+|||++++|+||||+|||||+|+|+|||+.||||||+|+|+|||||++.++|||| |+++||++. ++ |+.|.
T Consensus 80 aaGi~~~~ArtiGI~VD~RR~n~s~Esl~~Nv~rLk~y~skLvlFPrk~~k~kkG~~gip~Dss~ee~~~~~a~~q~~g~ 159 (212)
T PTZ00352 80 AAGLNAQAARSIGIAVDHRRRNRSQESLNLNVKRLKAYLSKLVLFPRKGKKPKKGFAGIPADTSKEEVVALPVKQNKNSE 159 (212)
T ss_pred HcCCCHHHhcccceeeccccccCcHHHHHHHHHHHHHHHHheeeecCCCCccccCCCCCCCCCCHHHHHHHHHHHhhcCc
Confidence 5899999999999999999999999999999999999999999999999999999 999999988 77 89999
Q ss_pred cCCCCCCCCcccccccCcccccchHHHHHHHHHhhhhhhhhhhhHHHHHHHh
Q 041207 72 YMPIAPERPTVELVKVTQDMKSFKAYDKLRIERVNERHFGARMKKAAEAEKE 123 (126)
Q Consensus 72 v~Pi~~~~~~~~~r~it~eek~~~ay~~LR~ar~~~r~~G~r~kra~~~ae~ 123 (126)
+|||.+..+.++++.||+||++|+||.+||+||+++|++|+|+|+++++++.
T Consensus 160 vmPi~~~~~~~~~r~it~eek~~~Ay~tLR~aR~~ar~~G~r~kra~~k~~~ 211 (212)
T PTZ00352 160 VIPFQRTPKREKARVITKEERAFNAYRTLRQAKLNAKFVGKKEKKKQAKEKK 211 (212)
T ss_pred eecccccccccccccCCHHHHHhhHHHHHHHHHHHHHHhhHHHHHHHHhhcc
Confidence 9999999999999999999999999999999999999999999999988763
No 3
>PTZ00192 60S ribosomal protein L13; Provisional
Probab=100.00 E-value=7.5e-50 Score=318.82 Aligned_cols=119 Identities=42% Similarity=0.623 Sum_probs=113.2
Q ss_pred CCCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeecCCccccccCCCCHHHhhhhhh---------ccCc
Q 041207 1 AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAGDSAPEELATATQ---------VQGP 71 (126)
Q Consensus 1 aAGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPrk~~kpkkGDs~~ee~~~a~q---------~~~~ 71 (126)
+|||++++|+||||+|||||+|+|+||||.|||||++|+|+|||||++.++|||||+++||++.++| +.|.
T Consensus 87 ~aGi~~~~ArtiGI~VD~RR~n~s~Esl~~Nv~rLk~Y~skLilFPrk~~k~kkgds~~ee~k~a~Q~~~~~~~~~~~g~ 166 (218)
T PTZ00192 87 AAGLNPRFARTIGIRVDRRRKNKSEEGMNVNVQRLKTYMSKLVLFPMNHKKVQKGEAKEEEVKAATQDRSRFGDAAVGGV 166 (218)
T ss_pred HcCCCHHHhcccceeeccccccccHHHHHHHHHHHHHHHHheeeeccccCCCCCCCCCHHHHHHHHhhhcccccccccCc
Confidence 5899999999999999999999999999999999999999999999999999999999999999999 6689
Q ss_pred cCCCCCCCCcccccccCcccccchHHHHHHHHHhhhhhhhhhhhHHHHHHHhh
Q 041207 72 YMPIAPERPTVELVKVTQDMKSFKAYDKLRIERVNERHFGARMKKAAEAEKEE 124 (126)
Q Consensus 72 v~Pi~~~~~~~~~r~it~eek~~~ay~~LR~ar~~~r~~G~r~kra~~~ae~~ 124 (126)
+||| .++++.||++|++|+||.+||+||+++|++|+|+|+|++++..+
T Consensus 167 v~Pi-----~~~~~~it~eek~~~Ay~~LR~aR~~~r~~G~r~krak~~~~~~ 214 (218)
T PTZ00192 167 VTPS-----REAPRVVSKEERSKNVYAFLKKNHSAVRFFGVRSRRAARKEAKK 214 (218)
T ss_pred cccc-----ccccccCCHHHHHhhHHHHHHHHHHHhHHhhHHHHHHHHHHHhh
Confidence 9999 47899999999999999999999999999999999998876543
No 4
>PF01294 Ribosomal_L13e: Ribosomal protein L13e; InterPro: IPR001380 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 [, ]. The ribosomal protein L13e is widely found in vertebrates [], Drosophila melanogaster, plants, yeast, amongst others.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_U 4A1B_U 4A1D_U 4A19_U.
Probab=100.00 E-value=5e-45 Score=284.73 Aligned_cols=103 Identities=56% Similarity=0.834 Sum_probs=66.5
Q ss_pred CCCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeecCCccccccCCCCHHHhhhhhhccCccCCCCCCCC
Q 041207 1 AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAGDSAPEELATATQVQGPYMPIAPERP 80 (126)
Q Consensus 1 aAGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPrk~~kpkkGDs~~ee~~~a~q~~~~v~Pi~~~~~ 80 (126)
+|||+.++|+||||+|||||+|+|+|||+.|||||++|+|||||||++.++||+||+++||++.|+|+.|++|||.+..+
T Consensus 77 ~aGi~~~~A~tiGI~VD~RR~n~s~Esl~~Nv~RLkeY~sklilfPrk~~~~kkGdss~ee~k~a~q~~~~v~Pi~~~~~ 156 (179)
T PF01294_consen 77 AAGISKKYARTIGISVDHRRKNKSEESLQANVQRLKEYKSKLILFPRKAKKPKKGDSSAEELKLATQLKGPVMPIRKVKK 156 (179)
T ss_dssp HHT--HHHHHHHTB-B-TT----SHHHHHHHHHHHHHHHHT-----SSS---TTT--TTHHHH-----HHHHS-------
T ss_pred HcCCChHHccccCeeeccccCCccHHHHHHHHHHHHhhhhhceeecCccccccccCCCHHHHHHHHhhcCceeeecCCcC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCcccccchHHHHHHHH
Q 041207 81 TVELVKVTQDMKSFKAYDKLRIE 103 (126)
Q Consensus 81 ~~~~r~it~eek~~~ay~~LR~a 103 (126)
.++++.||+||++|+||.+||+|
T Consensus 157 ~~~~r~it~eek~~~af~~LR~a 179 (179)
T PF01294_consen 157 KEKARAITEEEKKFSAFRTLRMA 179 (179)
T ss_dssp ----HHHHHHHTTS-HHHHHHHH
T ss_pred ccccccCCHHHhhhhHHHHHhcC
Confidence 99999999999999999999986
No 5
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=99.79 E-value=2.7e-20 Score=130.34 Aligned_cols=39 Identities=44% Similarity=0.571 Sum_probs=37.4
Q ss_pred CCCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcce
Q 041207 1 AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLV 43 (126)
Q Consensus 1 aAGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLi 43 (126)
+|||++++|+||||+|||||+|+|+| ||||||+|+|+|=
T Consensus 41 aaGi~~~~ArtiGI~VD~RRrn~~~e----NVerLk~y~skL~ 79 (83)
T PRK12277 41 AAGLDIKNARKLGIRVDKRRKTVHEE----NVEALKKFLEQLG 79 (83)
T ss_pred HcCCCHHHhcccCeeecccccCCCHH----HHHHHHHHHHHhc
Confidence 59999999999999999999999988 9999999999984
No 6
>COG4352 RPL13 Ribosomal protein L13E [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=1.5e-17 Score=121.80 Aligned_cols=46 Identities=46% Similarity=0.811 Sum_probs=45.2
Q ss_pred CCCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeec
Q 041207 1 AAGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFP 46 (126)
Q Consensus 1 aAGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfP 46 (126)
+||++.+.||+|||+|||||+|.++|++++||+||++|++++|+||
T Consensus 68 aAGL~~~~AR~LGI~VD~RRr~~~~en~eal~k~ik~ll~~~~~~p 113 (113)
T COG4352 68 AAGLSARKARTLGIAVDHRRRNRNPENFEALVKRIKELLEKIIVFP 113 (113)
T ss_pred HcCcCHHHHHhhCcceehhhccCCHHHHHHHHHHHHHHHhcCccCC
Confidence 5899999999999999999999999999999999999999999998
No 7
>PF13318 DUF4089: Protein of unknown function (DUF4089)
Probab=56.08 E-value=3.1 Score=26.48 Aligned_cols=36 Identities=22% Similarity=0.519 Sum_probs=32.4
Q ss_pred ccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeecC
Q 041207 8 LAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPR 47 (126)
Q Consensus 8 ~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPr 47 (126)
+|..+|..+|.-++ .++..|.+|+..+-+=|.=||-
T Consensus 5 ~a~llgL~l~~~~r----~~V~~n~~ri~~mA~~v~~fpL 40 (50)
T PF13318_consen 5 MAALLGLPLDEEWR----PGVVANFERIAAMAQLVMEFPL 40 (50)
T ss_pred HHHHcCCCCCHHHH----HHHHHHHHHHHHHHHHHHcCCC
Confidence 46779999999988 9999999999999998888887
No 8
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=50.88 E-value=6.4 Score=28.14 Aligned_cols=34 Identities=32% Similarity=0.404 Sum_probs=27.3
Q ss_pred CCCCCCccCccCeeeccCCCCCchhhHHHHHHHHHhhhhcce
Q 041207 2 AGIPKKLAPTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLV 43 (126)
Q Consensus 2 AGi~~k~ArtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLi 43 (126)
+|||..++-.| .+-+.|.+..||+.|..|.+..|
T Consensus 81 ~GLp~~l~~~l--------~g~d~e~~~~~v~~l~~~~~~~v 114 (125)
T PF14265_consen 81 KGLPAELADFL--------VGDDEEETKANVKALKKLFNKAV 114 (125)
T ss_pred cCCCHHHHHHH--------hCCCHHHHHHHHHHHHHHHHHHH
Confidence 57777776666 47789999999999999876654
No 9
>smart00563 PlsC Phosphate acyltransferases. Function in phospholipid biosynthesis and have either glycerolphosphate, 1-acylglycerolphosphate, or 2-acylglycerolphosphoethanolamine acyltransferase activities. Tafazzin, the product of the gene mutated in patients with Barth syndrome, is a member of this family.
Probab=34.34 E-value=41 Score=21.91 Aligned_cols=36 Identities=19% Similarity=0.376 Sum_probs=25.2
Q ss_pred CeeeccCCCCCchhhHHHHHHHHHhhhhcceeecCCc
Q 041207 13 GVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRA 49 (126)
Q Consensus 13 GIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPrk~ 49 (126)
.|.||........+++..-.+-|+. ..-+++||-..
T Consensus 50 ~~~v~~~~~~~~~~~~~~~~~~l~~-~~~~~ifPeG~ 85 (118)
T smart00563 50 AIFIDRENGRLARAALREAVRLLRD-GGWLLIFPEGT 85 (118)
T ss_pred CeEEeCCCcHHHHHHHHHHHHHHhC-CCEEEEeCCcc
Confidence 3777776655677777766665654 56689999865
No 10
>PLN02510 probable 1-acyl-sn-glycerol-3-phosphate acyltransferase
Probab=34.02 E-value=43 Score=29.01 Aligned_cols=37 Identities=16% Similarity=0.299 Sum_probs=26.1
Q ss_pred CeeeccCCCCCchhhHHHHHHHHHhhhhc--ceeecCCcc
Q 041207 13 GVSVDHRRKNRSLEGLQSNVQRLKTYKAK--LVVFPRRAR 50 (126)
Q Consensus 13 GIaVD~RR~N~S~Esl~~NVqRLKeY~sk--LilfPrk~~ 50 (126)
+|.|| |......+.++.-+++++++... |+|||-...
T Consensus 145 ~I~v~-R~~~~D~~~l~~~l~~lk~~~~~~~LvIFPEGTR 183 (374)
T PLN02510 145 FIPVE-RKWEVDEPNIRQMLSSFKDPRDPLWLALFPEGTD 183 (374)
T ss_pred Ceeee-CCccccHHHHHHHHHHHhccCCCcEEEEeCCcCC
Confidence 57776 33344567888888888876544 899998654
No 11
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=32.59 E-value=35 Score=22.98 Aligned_cols=23 Identities=35% Similarity=0.485 Sum_probs=15.8
Q ss_pred HHHHHhhhhcc------eeecCCccccccCCCC
Q 041207 32 VQRLKTYKAKL------VVFPRRARKFKAGDSA 58 (126)
Q Consensus 32 VqRLKeY~skL------ilfPrk~~kpkkGDs~ 58 (126)
+.||..|+.++ .|-|| |+++||.
T Consensus 2 i~klq~yLr~~f~n~~i~v~~r----pk~~dsa 30 (63)
T PF11324_consen 2 IKKLQAYLRRTFGNPGITVKAR----PKKDDSA 30 (63)
T ss_pred hHHHHHHHHHHhCCCceEEEcC----CCCCCce
Confidence 35788887765 45555 7888875
No 12
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=32.07 E-value=26 Score=29.20 Aligned_cols=46 Identities=26% Similarity=0.294 Sum_probs=38.4
Q ss_pred CccCccCe---eeccCCCCCchhhHHHHHHHHHhhhhcceeecCCccccccCCC
Q 041207 7 KLAPTIGV---SVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPRRARKFKAGDS 57 (126)
Q Consensus 7 k~ArtIGI---aVD~RR~N~S~Esl~~NVqRLKeY~skLilfPrk~~kpkkGDs 57 (126)
-+|++||- +.|++= ..|..||..||=-+=-|.+|-.+++.|.-|.+
T Consensus 36 vv~rp~~~f~s~~d~~Y-----~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~ 84 (239)
T KOG0304|consen 36 VVARPIGTFRSSDDYHY-----QTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTD 84 (239)
T ss_pred eeeecCccccCChHHHH-----HHHHhchhhhhhhheeeeeeccCCCCCCCCCc
Confidence 36788885 667665 68999999999999999999999999987754
No 13
>cd07988 LPLAT_ABO13168-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are uncharacterized phospholipid/glycerol acyltransferases such as the Acinetobacter baumannii ATCC 17978 locus ABO13168 putative acyltransferase, and similar proteins.
Probab=30.98 E-value=94 Score=23.08 Aligned_cols=59 Identities=17% Similarity=0.214 Sum_probs=31.4
Q ss_pred CeeeccCCCCCchhhHHHHHHHHHhhhh--cceeecCCccccccCCCCHHHhhhhhhccCccCCCC
Q 041207 13 GVSVDHRRKNRSLEGLQSNVQRLKTYKA--KLVVFPRRARKFKAGDSAPEELATATQVQGPYMPIA 76 (126)
Q Consensus 13 GIaVD~RR~N~S~Esl~~NVqRLKeY~s--kLilfPrk~~kpkkGDs~~ee~~~a~q~~~~v~Pi~ 76 (126)
.|.||... ..++++.-++.|++ .+ -|+|||-...-+ -+.-..--...|.+...+|+|+.
T Consensus 71 ~i~V~r~~---~~~~~~~~~~~l~~-g~~~~l~IFPEGtR~~-~~~fk~G~~~lA~~~~~PIvPv~ 131 (163)
T cd07988 71 GIPVDRSR---AGGLVEQVVEEFRR-REEFVLAIAPEGTRSK-VDKWKTGFYHIARGAGVPILLVY 131 (163)
T ss_pred CEEeEcCC---cccHHHHHHHHHHh-CCCcEEEEeCCCCCCC-CcChhhHHHHHHHHcCCCEEEEE
Confidence 47888332 33567777777776 33 389999865322 11111111233444445677764
No 14
>cd07573 CPA N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases). CPA (EC 3.5.1.53, also known as N-carbamoylputrescine amidase and carbamoylputrescine hydrolase) converts N-carbamoylputrescine to putrescine, a step in polyamine biosynthesis in plants and bacteria. This subgroup includes Arabidopsis thaliana CPA, also known as nitrilase-like 1 (NLP1), and Pseudomonas aeruginosa AguB. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 11. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer; P. aeruginosa AugB is a homohexamer, Arabidopsis thaliana NLP1 is a homooctomer.
Probab=27.16 E-value=48 Score=25.98 Aligned_cols=23 Identities=13% Similarity=0.257 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHhhhh-------cceeecCC
Q 041207 26 EGLQSNVQRLKTYKA-------KLVVFPRR 48 (126)
Q Consensus 26 Esl~~NVqRLKeY~s-------kLilfPrk 48 (126)
...+.|++++.++.. .|||||--
T Consensus 12 ~d~~~n~~~~~~~i~~A~~~gadlivfPE~ 41 (284)
T cd07573 12 EDPEANLAKAEELVREAAAQGAQIVCLQEL 41 (284)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCcEEEcccc
Confidence 456789999999875 78999984
No 15
>PRK13286 amiE acylamide amidohydrolase; Provisional
Probab=26.61 E-value=60 Score=27.51 Aligned_cols=25 Identities=20% Similarity=0.410 Sum_probs=20.5
Q ss_pred chhhHHHHHHHHHhhh---------hcceeecCC
Q 041207 24 SLEGLQSNVQRLKTYK---------AKLVVFPRR 48 (126)
Q Consensus 24 S~Esl~~NVqRLKeY~---------skLilfPrk 48 (126)
+.+.+..|++|+.+.. ..|||||=-
T Consensus 27 ~~~di~~Nl~~i~~~i~~a~~~~~gadLVVfPE~ 60 (345)
T PRK13286 27 TKAEVLENARKIADMIVGMKQGLPGMDLVIFPEY 60 (345)
T ss_pred CHHHHHHHHHHHHHHHHHHHhcCCCCcEEEcCCc
Confidence 4468999999998865 589999985
No 16
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=26.43 E-value=73 Score=18.35 Aligned_cols=17 Identities=35% Similarity=0.397 Sum_probs=12.5
Q ss_pred hhhHHHHHHHHHhhhhc
Q 041207 25 LEGLQSNVQRLKTYKAK 41 (126)
Q Consensus 25 ~Esl~~NVqRLKeY~sk 41 (126)
.|.-..--+||++|.+|
T Consensus 11 ~ea~r~reeRla~y~aK 27 (28)
T PF10587_consen 11 EEAERIREERLAAYAAK 27 (28)
T ss_pred HHHHHHHHHHHHHHHcc
Confidence 45555667999999876
No 17
>cd07576 R-amidase_like Pseudomonas sp. MCI3434 R-amidase and related proteins (putative class 13 nitrilases). Pseudomonas sp. MCI3434 R-amidase hydrolyzes (R,S)-piperazine-2-tert-butylcarboxamide to form (R)-piperazine-2-carboxylic acid. It does so with strict R-stereoselectively. Its preferred substrates are carboxamide compounds which have the amino or imino group connected to their beta- or gamma-carbon. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), class 13 represents proteins that at the time were difficult to place in a distinct similarity group. It has been suggested that this subgroup represents a new class. Members of the nitrilase superfamily generally form homomeric compl
Probab=26.35 E-value=57 Score=24.96 Aligned_cols=23 Identities=35% Similarity=0.563 Sum_probs=17.9
Q ss_pred hhHHHHHHHHHhhhh-------cceeecCC
Q 041207 26 EGLQSNVQRLKTYKA-------KLVVFPRR 48 (126)
Q Consensus 26 Esl~~NVqRLKeY~s-------kLilfPrk 48 (126)
..++.|++++.++.. .|||||--
T Consensus 12 ~d~~~n~~~i~~~i~~a~~~ga~lvv~PE~ 41 (254)
T cd07576 12 GDVAANLARLDEAAARAAAAGADLLVFPEL 41 (254)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCEEEccCc
Confidence 567889888877654 68999984
No 18
>cd07582 nitrilase_4 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer.
Probab=26.19 E-value=61 Score=25.96 Aligned_cols=26 Identities=23% Similarity=0.451 Sum_probs=20.6
Q ss_pred CchhhHHHHHHHHHhhh------------hcceeecCC
Q 041207 23 RSLEGLQSNVQRLKTYK------------AKLVVFPRR 48 (126)
Q Consensus 23 ~S~Esl~~NVqRLKeY~------------skLilfPrk 48 (126)
.+...++.|++++.++. ..|||||--
T Consensus 14 ~~~~d~~~Nl~~~~~~i~~A~~~~~~~~gadlivfPE~ 51 (294)
T cd07582 14 EDRADILANIDRINEQIDAAVGFSGPGLPVRLVVLPEY 51 (294)
T ss_pred cChhhHHHHHHHHHHHHHHHHHhcccCCCceEEEcCcc
Confidence 35577899999998762 699999974
No 19
>cd07570 GAT_Gln-NAD-synth Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases). Glutamine-dependent NAD synthetases are bifunctional enzymes, which have an N-terminal GAT domain and a C-terminal NAD+ synthetase domain. The GAT domain is a glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to L-glutamate and ammonia. The ammonia is used by the NAD+ synthetase domain in the ATP-dependent amidation of nicotinic acid adenine dinucleotide. Glutamine aminotransferases are categorized depending on their active site residues into different unrelated classes. This class of GAT domain belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this sub
Probab=26.04 E-value=56 Score=25.27 Aligned_cols=23 Identities=35% Similarity=0.557 Sum_probs=18.3
Q ss_pred hHHHHHHHHHhhh-------hcceeecCCc
Q 041207 27 GLQSNVQRLKTYK-------AKLVVFPRRA 49 (126)
Q Consensus 27 sl~~NVqRLKeY~-------skLilfPrk~ 49 (126)
..+.|++++.++. ..|||||--.
T Consensus 13 d~~~N~~~~~~~i~~A~~~gadlvvfPE~~ 42 (261)
T cd07570 13 DLEGNAEKILEAIREAKAQGADLVVFPELS 42 (261)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCEEEccchh
Confidence 4678999888775 6899999853
No 20
>PF00795 CN_hydrolase: Carbon-nitrogen hydrolase The Prosite family is specific to nitrilases The Prosite family is specific to UPF0012; InterPro: IPR003010 This family contains nitrilases that break carbon-nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production []. They all have distinct substrate specificity and include cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function. Sequence conservation over the entire length, as well as the similarity in the reactions catalyzed by the known enzymes in this family, points to a common catalytic mechanism. They have an invariant cysteine that is part of the catalytic site in nitrilases. Another highly conserved motif includes an invariant glutamic acid that might also be involved in catalysis [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0006807 nitrogen compound metabolic process; PDB: 2E2L_D 2E2K_D 2DYV_A 2DYU_B 3KLC_B 3IW3_A 3KI8_A 3IVZ_A 1EMS_A 2GGK_B ....
Probab=24.02 E-value=77 Score=22.87 Aligned_cols=25 Identities=32% Similarity=0.498 Sum_probs=18.8
Q ss_pred chhhHHHHHHHHHhhh-------hcceeecCC
Q 041207 24 SLEGLQSNVQRLKTYK-------AKLVVFPRR 48 (126)
Q Consensus 24 S~Esl~~NVqRLKeY~-------skLilfPrk 48 (126)
+...++.|.+++..+. ..|||||--
T Consensus 12 ~~~~~~~n~~~i~~~~~~a~~~~~dlvv~PE~ 43 (186)
T PF00795_consen 12 SWGDPEENLKKILSLIEEAARQGADLVVFPEM 43 (186)
T ss_dssp STTHHHHHHHHHHHHHHHHHHTTESEEEEETT
T ss_pred ccCCHHHHHHHHHHHHHHHHHCCCCEEEcCcc
Confidence 4467778888877765 679999974
No 21
>cd07584 nitrilase_6 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer.
Probab=23.70 E-value=68 Score=24.75 Aligned_cols=23 Identities=17% Similarity=0.421 Sum_probs=18.1
Q ss_pred hhHHHHHHHHHhhhh-------cceeecCC
Q 041207 26 EGLQSNVQRLKTYKA-------KLVVFPRR 48 (126)
Q Consensus 26 Esl~~NVqRLKeY~s-------kLilfPrk 48 (126)
..++.|++++..+.. .|||||--
T Consensus 12 ~d~~~n~~~~~~~i~~a~~~ga~liv~PE~ 41 (258)
T cd07584 12 GDVKANLKKAAELCKEAAAEGADLICFPEL 41 (258)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCEEEcccc
Confidence 356889999888764 79999974
No 22
>PLN02380 1-acyl-sn-glycerol-3-phosphate acyltransferase
Probab=23.70 E-value=73 Score=27.70 Aligned_cols=36 Identities=31% Similarity=0.445 Sum_probs=26.0
Q ss_pred eeeccCCCCCchhhHHHHHHHHHhhhhc--ceeecCCcc
Q 041207 14 VSVDHRRKNRSLEGLQSNVQRLKTYKAK--LVVFPRRAR 50 (126)
Q Consensus 14 IaVD~RR~N~S~Esl~~NVqRLKeY~sk--LilfPrk~~ 50 (126)
|.|| |...+..+.++.-.++|++|... |++||-...
T Consensus 138 IfId-R~~~~d~~~l~~~~~~l~~~~~~~wllIFPEGTR 175 (376)
T PLN02380 138 VFLE-RSWAKDENTLKSGFQRLKDFPRPFWLALFVEGTR 175 (376)
T ss_pred EEec-CCchhHHHHHHHHHHHHhhCCCccEEEEecCcCC
Confidence 5566 33345578888888999987654 999998653
No 23
>cd07581 nitrilase_3 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer.
Probab=23.47 E-value=60 Score=24.94 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=19.4
Q ss_pred hhHHHHHHHHHhhhh-------cceeecCCc
Q 041207 26 EGLQSNVQRLKTYKA-------KLVVFPRRA 49 (126)
Q Consensus 26 Esl~~NVqRLKeY~s-------kLilfPrk~ 49 (126)
..++.|++++.++.. .|||||--.
T Consensus 10 ~d~~~n~~~~~~~i~~a~~~g~dlivfPE~~ 40 (255)
T cd07581 10 GDKEENLEKVRRLLAEAAAAGADLVVFPEYT 40 (255)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCEEECcchh
Confidence 578899999888765 599999854
No 24
>cd07577 Ph0642_like Pyrococcus horikoshii Ph0642 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases). Uncharacterized subgroup of the nitrilase superfamily. This superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. Pyrococcus horikoshii Ph0642 is a hypothetical protein belonging to this subgroup. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). This subgroup was classified as belonging to class 13, which represents proteins that at the time were difficult to place in a distinct similarity group. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer.
Probab=22.85 E-value=70 Score=24.83 Aligned_cols=23 Identities=17% Similarity=0.473 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHhhhh----cceeecCC
Q 041207 26 EGLQSNVQRLKTYKA----KLVVFPRR 48 (126)
Q Consensus 26 Esl~~NVqRLKeY~s----kLilfPrk 48 (126)
.....|++++.++.. .|||||--
T Consensus 12 ~d~~~N~~~~~~~i~~a~adlvvfPE~ 38 (259)
T cd07577 12 GEVEKNLKKVESLIKGVEADLIVLPEL 38 (259)
T ss_pred CCHHHHHHHHHHHHHHhCCCEEEcccc
Confidence 467889999988875 79999984
No 25
>KOG3995 consensus 3-hydroxyanthranilate oxygenase HAAO [Amino acid transport and metabolism]
Probab=22.73 E-value=38 Score=28.46 Aligned_cols=22 Identities=36% Similarity=0.756 Sum_probs=18.4
Q ss_pred CCCccCccCeeeccCCCCCchh
Q 041207 5 PKKLAPTIGVSVDHRRKNRSLE 26 (126)
Q Consensus 5 ~~k~ArtIGIaVD~RR~N~S~E 26 (126)
+.++|-||||-|.-+|.|.-..
T Consensus 95 PqRFantvGlVVEr~R~~tE~D 116 (279)
T KOG3995|consen 95 PQRFANTVGLVVERRRLETELD 116 (279)
T ss_pred hhhhccceeEEEEeccCCCccc
Confidence 4689999999999999986544
No 26
>cd07574 nitrilase_Rim1_like Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases). Some members of this subgroup are implicated in post-translational modification, as they contain an N-terminal GCN5-related N-acetyltransferase (GNAT) protein RimI family domain. The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 12. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer.
Probab=22.14 E-value=71 Score=25.02 Aligned_cols=24 Identities=21% Similarity=0.422 Sum_probs=18.0
Q ss_pred hhHHHHHHHHHhhhh-------cceeecCCc
Q 041207 26 EGLQSNVQRLKTYKA-------KLVVFPRRA 49 (126)
Q Consensus 26 Esl~~NVqRLKeY~s-------kLilfPrk~ 49 (126)
..++.|++++..|.. .|||||--.
T Consensus 14 ~~~~~n~~~i~~~i~~A~~~gadlivfPE~~ 44 (280)
T cd07574 14 ASFEEFAAKVEYWVAEAAGYGADLLVFPEYF 44 (280)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCEEECchHh
Confidence 456788888877655 699999853
No 27
>PF00058 Ldl_recept_b: Low-density lipoprotein receptor repeat class B; InterPro: IPR000033 The low-density lipoprotein receptor (LDLR) is the major cholesterol-carrying lipoprotein of plasma, acting to regulate cholesterol homeostasis in mammalian cells. The LDL receptor binds LDL and transports it into cells by acidic endocytosis. In order to be internalized, the receptor-ligand complex must first cluster into clathrin-coated pits. Once inside the cell, the LDLR separates from its ligand, which is degraded in the lysosomes, while the receptor returns to the cell surface []. The internal dissociation of the LDLR with its ligand is mediated by proton pumps within the walls of the endosome that lower the pH. The LDLR is a multi-domain protein, containing: The ligand-binding domain contains seven or eight 40-amino acid LDLR class A (cysteine-rich) repeats, each of which contains a coordinated calcium ion and six cysteine residues involved in disulphide bond formation []. Similar domains have been found in other extracellular and membrane proteins []. The second conserved region contains two EGF repeats, followed by six LDLR class B (YWTD) repeats, and another EGF repeat. The LDLR class B repeats each contain a conserved YWTD motif, and is predicted to form a beta-propeller structure []. This region is critical for ligand release and recycling of the receptor []. The third domain is rich in serine and threonine residues and contains clustered O-linked carbohydrate chains. The fourth domain is the hydrophobic transmembrane region. The fifth domain is the cytoplasmic tail that directs the receptor to clathrin-coated pits. LDLR is closely related in structure to several other receptors, including LRP1, LRP1b, megalin/LRP2, VLDL receptor, lipoprotein receptor, MEGF7/LRP4, and LRP8/apolipoprotein E receptor2); these proteins participate in a wide range of physiological processes, including the regulation of lipid metabolism, protection against atherosclerosis, neurodevelopment, and transport of nutrients and vitamins []. This entry represents the LDLR classB (YWTD) repeat, the structure of which has been solved []. The six YWTD repeats together fold into a six-bladed beta-propeller. Each blade of the propeller consists of four antiparallel beta-strands; the innermost strand of each blade is labeled 1 and the outermost strand, 4. The sequence repeats are offset with respect to the blades of the propeller, such that any given 40-residue YWTD repeat spans strands 24 of one propeller blade and strand 1 of the subsequent blade. This offset ensures circularization of the propeller because the last strand of the final sequence repeat acts as an innermost strand 1 of the blade that harbors strands 24 from the first sequence repeat. The repeat is found in a variety of proteins that include, vitellogenin receptor from Drosophila melanogaster, low-density lipoprotein (LDL) receptor [], preproepidermal growth factor, and nidogen (entactin).; PDB: 3S2K_A 3S8Z_A 3S8V_B 4A0P_A 3SOB_B 3S94_B 4DG6_A 3SOV_A 3SOQ_A 1NPE_A ....
Probab=21.99 E-value=36 Score=20.11 Aligned_cols=9 Identities=33% Similarity=0.534 Sum_probs=6.6
Q ss_pred CccCeeecc
Q 041207 10 PTIGVSVDH 18 (126)
Q Consensus 10 rtIGIaVD~ 18 (126)
.--||+|||
T Consensus 34 ~P~giaVD~ 42 (42)
T PF00058_consen 34 HPEGIAVDW 42 (42)
T ss_dssp SEEEEEEET
T ss_pred CcCEEEECC
Confidence 345899986
No 28
>COG1999 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]
Probab=21.96 E-value=73 Score=25.03 Aligned_cols=28 Identities=32% Similarity=0.450 Sum_probs=21.3
Q ss_pred CccCeeeccCCCCCchhhHHHHHHHHHhhhhcceeecC
Q 041207 10 PTIGVSVDHRRKNRSLEGLQSNVQRLKTYKAKLVVFPR 47 (126)
Q Consensus 10 rtIGIaVD~RR~N~S~Esl~~NVqRLKeY~skLilfPr 47 (126)
+-+=|+||+.|-. -++|++|.+ +=.+|+
T Consensus 106 ~vv~itvDPerDt---------p~~lk~Y~~-~~~~~~ 133 (207)
T COG1999 106 QVVFITVDPERDT---------PEVLKKYAE-LNFDPR 133 (207)
T ss_pred EEEEEEECCCCCC---------HHHHHHHhc-ccCCCC
Confidence 3466999999963 789999999 544554
No 29
>cd07197 nitrilase Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes. This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and
Probab=20.55 E-value=89 Score=23.56 Aligned_cols=23 Identities=17% Similarity=0.361 Sum_probs=18.2
Q ss_pred hhHHHHHHHHHhhhh-------cceeecCC
Q 041207 26 EGLQSNVQRLKTYKA-------KLVVFPRR 48 (126)
Q Consensus 26 Esl~~NVqRLKeY~s-------kLilfPrk 48 (126)
..++.|++|+..+.. .|||||--
T Consensus 11 ~~~~~n~~~~~~~i~~a~~~g~dlvvfPE~ 40 (253)
T cd07197 11 GDVEANLAKALRLIKEAAEQGADLIVLPEL 40 (253)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEcCCc
Confidence 567889998887765 58999974
Done!