GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas simiae WCS417

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate GFF4563 PS417_23355 4-aminobutyrate aminotransferase

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__WCS417:GFF4563
          Length = 416

 Score =  666 bits (1719), Expect = 0.0
 Identities = 324/416 (77%), Positives = 369/416 (88%)

Query: 1   MNQESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQ 60
           M+ E+ISQSI+IVHPI+LSHG+NAEVWDT GKRYIDFVGGIGVLNLGHC+P VV+AI+ Q
Sbjct: 1   MSHETISQSISIVHPISLSHGKNAEVWDTSGKRYIDFVGGIGVLNLGHCHPGVVDAIRDQ 60

Query: 61  ATRLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKR 120
           ATRLTHYAFNAAPH PY+ LM++L+ F+PV YP++GMLTNSGAEAAENALK+ RGATG+ 
Sbjct: 61  ATRLTHYAFNAAPHAPYVELMDRLTAFIPVDYPISGMLTNSGAEAAENALKIVRGATGRT 120

Query: 121 AIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDR 180
           A+IAFDG FHGRTLATLNLNGKVAPYKQ+VG LPGPVYHLPYPSAD GVTC +ALKAMDR
Sbjct: 121 AVIAFDGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVYHLPYPSADNGVTCAEALKAMDR 180

Query: 181 LFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTG 240
           LFSVE+ V DVA FI EPVQGEGGFLALD  FAQALRRFC+E  IL+I DEIQSGFGRTG
Sbjct: 181 LFSVEIDVSDVACFIIEPVQGEGGFLALDIEFAQALRRFCNENNILLIADEIQSGFGRTG 240

Query: 241 QRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAAL 300
           +RFAF RLGIEPDL+LL KSIAGG+PLGAVVGRK LM  LPKGGLGGTYSGNPI+CAAAL
Sbjct: 241 ERFAFSRLGIEPDLILLGKSIAGGVPLGAVVGRKALMDNLPKGGLGGTYSGNPIACAAAL 300

Query: 301 ASLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPA 360
           A+L  MTDE+L+ WG +QE+AIVSRY+ W+A GL+PY+GRLTGVG+MRGIE ANADG+PA
Sbjct: 301 ATLDAMTDEHLSAWGSQQEEAIVSRYQTWRAHGLTPYLGRLTGVGSMRGIELANADGTPA 360

Query: 361 PAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAELN 416
           P QL +++  AR  GLLLMPSGK+RHIIRLLAPLTIE  VLEEGL + E CL +L+
Sbjct: 361 PKQLTQLLGLARDAGLLLMPSGKSRHIIRLLAPLTIEPAVLEEGLTMFEACLKQLD 416


Lambda     K      H
   0.320    0.137    0.402 

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: 689
Number of extensions: 17
Number of successful extensions: 1
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: 416
Length of database: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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