GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Cupriavidus basilensis 4G11

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate RR42_RS14595 RR42_RS14595 2-aminoadipate aminotransferase

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__Cup4G11:RR42_RS14595
          Length = 395

 Score =  322 bits (826), Expect = 1e-92
 Identities = 174/395 (44%), Positives = 249/395 (63%), Gaps = 13/395 (3%)

Query: 23  SEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQY 82
           S +A  + +S IRE+LK+ E  +VIS AGGLP+P TFPV  + +    +   +   ALQY
Sbjct: 6   SRRAQQLTSSAIREILKVTERPEVISFAGGLPSPATFPVAAMEQAVARIFADNPQAALQY 65

Query: 83  GTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPT 142
             T+G+ PLR    E++ +R+ + + +V  + T+GSQQALDLI +V I+PG  ++VE P+
Sbjct: 66  AATEGYMPLR----EFIAKRHAVDVERV--LITTGSQQALDLIAKVMIDPGSPVLVETPS 119

Query: 143 YLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVT 202
           YL ALQAF  +EPEFV +P DD+     LL E L      G   + +Y +P FQNP G  
Sbjct: 120 YLGALQAFSLFEPEFVSVPGDDKS----LLPESLTPELTAG--ARFLYALPNFQNPTGRR 173

Query: 203 MNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAP 262
           M  +RR+ L+  A +   ++VED+PYGEL YSG+ +  + + + +G VIY+G+FSKILAP
Sbjct: 174 MPLERRQALVARARELGLLLVEDDPYGELSYSGDQLPSLLSMNPDG-VIYMGSFSKILAP 232

Query: 263 GFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRR 322
           G R+G++ A P    KL  AKQ+ DL T +F+Q +A++ V  G LD HIP I   Y  + 
Sbjct: 233 GLRLGFVIAPPELHFKLCQAKQASDLHTPSFTQRLAYEVVRDGLLDSHIPTIRTLYAAQC 292

Query: 323 DAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHR 382
            AML +L   MP+GV W  PEGGMF+W  LPEG+D+  +L++AV + VAYVPG  F+A  
Sbjct: 293 QAMLDSLARHMPEGVTWNAPEGGMFIWMELPEGLDSMEILQEAVNRNVAYVPGAPFYASN 352

Query: 383 DVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417
             +N +RL F  V  E+I +G+  L    +E + K
Sbjct: 353 PRRNALRLAFVTVAPERIEQGVAILGTLFREAIAK 387


Lambda     K      H
   0.318    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 481
Number of extensions: 20
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 395
Length adjustment: 31
Effective length of query: 386
Effective length of database: 364
Effective search space:   140504
Effective search space used:   140504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory