GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Pseudomonas fluorescens GW456-L13

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate PfGW456L13_4175 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::A0A060PQX5
         (417 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4175
           Transcriptional regulator, GntR family domain /
           Aspartate aminotransferase (EC 2.6.1.1)
          Length = 388

 Score =  240 bits (612), Expect = 6e-68
 Identities = 140/392 (35%), Positives = 213/392 (54%), Gaps = 15/392 (3%)

Query: 22  FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81
           FS++   +K+S +RE+L   +   V+S AGGLPA    P    AE+   +         Q
Sbjct: 3   FSERVSRLKSSLIREILAAAQRPQVMSFAGGLPAETMLPKVEWAEMPVSMG--------Q 54

Query: 82  YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141
           YG ++G   LR ALA   R    +P     +++ SGSQQ LDL  +++I+ G  +++EAP
Sbjct: 55  YGMSEGEPALREALAAEARA-LGVPCEASQVLVVSGSQQTLDLAAKLYIDKGTEILLEAP 113

Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201
           TYLAALQ F+ +  + + + L+ +G  +  L  +L++      +   +Y IPTFQNP+ V
Sbjct: 114 TYLAALQIFQLFGADCLTVSLEADGPNLTALRARLEQ-----HRPAFIYLIPTFQNPSAV 168

Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261
             SE +R  +  L  E+   ++ED PY EL + G    PI +       +Y GT SK L 
Sbjct: 169 RYSEAKRNAVAALLDEFGVTLIEDEPYRELTFDGGCATPIVSRLKRASWIYTGTVSKTLL 228

Query: 262 PGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPR 321
           PG R+G++ A P L   L   KQS DL TN   Q  A +++       H   + +FY+ R
Sbjct: 229 PGLRVGYLIASPDLFPHLLKLKQSADLHTNRVGQWQALQWIGTEKYQQHRSELRDFYRGR 288

Query: 322 RDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381
           RDA   ALE    +   W  P+GG+F W+ L +  DT+ +L  A+A  VA++PGE FF  
Sbjct: 289 RDAFQAALETHFSDLADWNVPQGGLFFWLKLKQPQDTRTLLNAALANDVAFMPGEPFFPE 348

Query: 382 RD-VKNTMRLNFTYVPEEKIREGIKRLAETIK 412
            D     +RLNF+++   ++ EG+KRLA  ++
Sbjct: 349 PDNHPGYLRLNFSHIDPARLDEGLKRLAAVVR 380


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: 391
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 388
Length adjustment: 31
Effective length of query: 386
Effective length of database: 357
Effective search space:   137802
Effective search space used:   137802
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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