GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Pseudomonas benzenivorans DSM 8628

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_090447976.1 BLS63_RS22185 alpha/beta hydrolase

Query= SwissProt::Q1J115
         (336 letters)



>NCBI__GCF_900100495.1:WP_090447976.1
          Length = 339

 Score = 48.1 bits (113), Expect = 3e-10
 Identities = 75/267 (28%), Positives = 108/267 (40%), Gaps = 45/267 (16%)

Query: 43  DVRVAYHTYGTPSDHAILVLHALTGTSAVHEWWPDFLGEGKPLDPTRDYIVCANVLGGCA 102
           +V++AY + G  SD  +L++  L G   +H  WPD +   +  D     I   N   G +
Sbjct: 35  EVQLAYQSIGRTSDPVLLMVMGLGG-QLIH--WPDEV-VARLCDQGFRVIRFDNRDVGLS 90

Query: 103 GSTGPAELPRVNGE----------DPPLTLRDMARVGRALLEELGVRRVSVIGASMGGML 152
             T  A    +  E            P  LRDMA     L++ LGVR+  V+GASMGGM+
Sbjct: 91  RWTHAAPPANLGYEALRYRLGLSVSAPYRLRDMAGDALGLMDALGVRQFHVLGASMGGMI 150

Query: 153 AYAWLLECPDLVDRAVII----GAPARHSPWAIGLNTAARNAIRAAPGGEGLKVARQIAM 208
           A       P  V    +I    GA    +P    L   A+   R AP       +R++A+
Sbjct: 151 AQHLADLAPQRVQSLTLIMTSSGAAGLPAPSPALLELLAK---REAP-------SREVAL 200

Query: 209 LSYRSPESFALTQSGWGTRRPGTPDITTYLEHQGEKLSTRF-----CERSYLALTGAMDR 263
                 E  A   +  G+  P   D    L  Q E    R       +R  LA+     R
Sbjct: 201 ------EQQADLLAALGS--PAVSDDRQALLQQAETAYDRAFNPEGVQRQLLAILAEPSR 252

Query: 264 FQPTDAELRSIRVPVLVVGISSDVLYP 290
            +     L  +R+P LVV  ++D L P
Sbjct: 253 VE----LLNRLRLPTLVVHGTADPLLP 275


Lambda     K      H
   0.320    0.138    0.429 

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: 277
Number of extensions: 9
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: 336
Length of database: 339
Length adjustment: 28
Effective length of query: 308
Effective length of database: 311
Effective search space:    95788
Effective search space used:    95788
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: 49 (23.5 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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