GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens GW456-L13

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)

Query= SwissProt::Q93R93
         (395 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301
          Length = 466

 Score =  238 bits (608), Expect = 2e-67
 Identities = 158/415 (38%), Positives = 226/415 (54%), Gaps = 49/415 (11%)

Query: 29  LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQ-AETLMAMPQTLPTP 87
           L + R +G  V D EG  +IDC+ G G   LGH +P V+EA+++  A+ L      L TP
Sbjct: 47  LALKRAKGIYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTP 106

Query: 88  MRGEFYRTLTAILPPELNRVFPVN----SGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143
           ++  F + L  +LPP L     +     +GT+A EAALK  R  TGR   ++   G+ G 
Sbjct: 107 VKDRFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVISFQGGYHGM 166

Query: 144 TMGSLSVTWEPKYREPFLPLV-EPVEFIPYN-----------------DVEALKRAVDEE 185
           + G+LS+      ++P   L+   V+F+PY                  ++  L+  +++ 
Sbjct: 167 SQGALSLMGSLGPKKPLGALLGSGVQFMPYPYDYRCPFGLGGAQGVKANLSYLENLLNDP 226

Query: 186 TA------AVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFA 239
            A      AVI+E VQGEGGV PA  ++LR  R IT++ G  LI+DEIQ+G  RTGK FA
Sbjct: 227 EAGVQLPAAVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSGFARTGKMFA 286

Query: 240 FEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIR 299
           FEH GI+PD++ ++KA+GG +PL V V R+ +   +P G H  TF GN +AMAAG A +R
Sbjct: 287 FEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLP-GAHAGTFRGNQMAMAAGCAVMR 345

Query: 300 YLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEKAA--------P 349
           YL   ++ E AA +G    E LR +    P++ ++RG GLM+G+EL +           P
Sbjct: 346 YLVEHKVCEHAAAMGERLAEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGALDAQGHPP 405

Query: 350 YIARL------EKEHRVLALQAG---PTVIRFLPPLVIEKEDLERVVEAVRAVLA 395
             ARL      E   R L L+ G     V+RFLPPLVI    ++RV E     LA
Sbjct: 406 AFARLAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGRALA 460


Lambda     K      H
   0.319    0.137    0.403 

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: 487
Number of extensions: 17
Number of successful extensions: 7
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: 395
Length of database: 466
Length adjustment: 32
Effective length of query: 363
Effective length of database: 434
Effective search space:   157542
Effective search space used:   157542
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 (21.7 bits)
S2: 51 (24.3 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