GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas fluorescens FW300-N2E2

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; EC 1.2.1.11; Aspartate-beta-semialdehyde dehydrogenase (uncharacterized)
to candidate Pf6N2E2_4232 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

Query= curated2:O67716
         (340 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4232
          Length = 329

 Score =  229 bits (585), Expect = 6e-65
 Identities = 126/333 (37%), Positives = 205/333 (61%), Gaps = 10/333 (3%)

Query: 4   RVAIVGATGEVGRTFLKVLEERNFPVDELVLYASERSEGKVLTFKGKEYTVKALNKENSF 63
           +VA+VG TG VG T L++LE  ++   E+V  AS RS GK L     E+ ++A + E   
Sbjct: 3   KVAVVGCTGAVGMTMLQLLENTDY---EVVCMASGRSAGKRLKVGQVEHLIEAFSVEGC- 58

Query: 64  KGIDIALFSAGGSTSKEWAPKFAKDGVVVIDNSSAWRMDPDVPLVVPEVNPEDVKDFKKK 123
              DI      G+ + E+  + A++  V IDNSSA+R  P +PL+VP +N +     K  
Sbjct: 59  ASCDIVFLCVSGAFALEYGERLAENAYV-IDNSSAFRYHPAIPLLVPPINGQRYMGEK-- 115

Query: 124 GIIANPNCSTIQMVVALKPIYDKAGIKRVVVSTYQAVSGAGAKAIEDLKNQTKAWCEGKE 183
            +IANPNCS+   ++ L P++   G++  ++STYQA SGAG  A+ +L+ + K++ +  +
Sbjct: 116 -LIANPNCSSAIALMVLGPLHQAFGLESAIISTYQAASGAGQPAMLELREKAKSFSDYGD 174

Query: 184 MPKAQKFPHQIAFNALPHIDVFFEDGYTKEENKMLYETRKIMHDENIKVSATCVRIPVFY 243
              ++ F H +AFN +P +D F  +GYT+EE K+++E RK++ +  + +S T VR+P   
Sbjct: 175 RDDSEHFAHNLAFNVIPQVDSFEANGYTREEMKVVWELRKVLDEPTLAISTTAVRVPTLR 234

Query: 244 GHSESISMETEKEI-SPEEAREVLKNAPGVIVIDNPQNNEYPMPIMAEGRDEVFVGRIRK 302
            H+ES+S+     I S E+ RE+L++APGV V+D P+   YPMP+ +  +  V VGRIR 
Sbjct: 235 SHAESLSLRFNTPIQSLEQVRELLRSAPGVEVVDEPEFGAYPMPMTSTYKHAVEVGRIRY 294

Query: 303 DRVF-EPGLSMWVVADNIRKGAATNAVQIAELL 334
           + ++ E GL +++  D + +GAA NA +I +L+
Sbjct: 295 NLIYGEHGLDLFISGDQLLRGAALNAFEIMQLI 327


Lambda     K      H
   0.316    0.134    0.386 

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: 202
Number of extensions: 9
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: 340
Length of database: 329
Length adjustment: 28
Effective length of query: 312
Effective length of database: 301
Effective search space:    93912
Effective search space used:    93912
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 (21.6 bits)
S2: 49 (23.5 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