GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Novosphingobium barchaimii LL02

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_059150560.1 V474_RS06080 aminotransferase class V-fold PLP-dependent enzyme

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>NCBI__GCF_001046635.1:WP_059150560.1
          Length = 402

 Score =  597 bits (1538), Expect = e-175
 Identities = 300/402 (74%), Positives = 334/402 (83%)

Query: 1   MKRRTGQDRSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQ 60
           MKR TGQDR+ T+NW+PAT+AIRGGT RSE GETSEALFLTSGYAYD A   AARF G++
Sbjct: 1   MKRTTGQDRTQTRNWRPATRAIRGGTWRSEMGETSEALFLTSGYAYDDAATVAARFMGEE 60

Query: 61  QGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAF 120
           +GMTYSRLQNPTV MLE+RIALLEGAEACR  A+GMAAMTAALLCQLSAGDH++  RAAF
Sbjct: 61  EGMTYSRLQNPTVAMLEERIALLEGAEACRTQATGMAAMTAALLCQLSAGDHMVTARAAF 120

Query: 121 GSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCA 180
           GSCRWL D  LP+FG+E TV+DA D   +  AIRPNTKVFFFETPANPTMDV DL  + A
Sbjct: 121 GSCRWLGDHLLPRFGVEVTVIDAGDLTAWEAAIRPNTKVFFFETPANPTMDVADLAGIAA 180

Query: 181 IARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNT 240
           IA+  GI TVVDNAF +PALQRPM+FG DVVAYSATK+MDGQGRVLAGAVCG+EEFIN+ 
Sbjct: 181 IAKAHGITTVVDNAFCSPALQRPMEFGIDVVAYSATKLMDGQGRVLAGAVCGSEEFINDK 240

Query: 241 LLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGRVPRVNFPGLPSH 300
           LLPF RNTGP LSPFNAWVVLKGLETLDLR ++QSENAL + +F+E RVP++  P L SH
Sbjct: 241 LLPFQRNTGPNLSPFNAWVVLKGLETLDLRAKKQSENALALGKFVEARVPKILHPWLDSH 300

Query: 301 PQHNLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHS 360
           PQ  LAM QM A GPIFS  LDGGR QA GLLD L LIDISNNIGDSRSLM HPASTTH 
Sbjct: 301 PQQALAMKQMDACGPIFSFVLDGGREQAWGLLDGLKLIDISNNIGDSRSLMCHPASTTHH 360

Query: 361 GVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGSVGL 402
            +  + R  MG+GEGMLR+NVGLED +DLI D DQAL  VGL
Sbjct: 361 NMGAEGREAMGIGEGMLRINVGLEDIDDLIEDFDQALTKVGL 402


Lambda     K      H
   0.319    0.134    0.396 

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: 551
Number of extensions: 14
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: 402
Length of database: 402
Length adjustment: 31
Effective length of query: 371
Effective length of database: 371
Effective search space:   137641
Effective search space used:   137641
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 Jul 26 2024. The underlying query database was built on Jul 25 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