GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metA in Paraburkholderia bryophila 376MFSha3.1

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate H281DRAFT_02214 H281DRAFT_02214 homoserine O-acetyltransferase

Query= SwissProt::Q2T284
         (381 letters)



>FitnessBrowser__Burk376:H281DRAFT_02214
          Length = 381

 Score =  697 bits (1800), Expect = 0.0
 Identities = 335/381 (87%), Positives = 360/381 (94%)

Query: 1   MESIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVA 60
           MESIG+VAP  MHF EPLRLQ+GS L +Y L+VETYG LNAARSNAVLVCHALNASHHVA
Sbjct: 1   MESIGIVAPQKMHFTEPLRLQNGSSLASYDLMVETYGTLNAARSNAVLVCHALNASHHVA 60

Query: 61  GVYADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARF 120
           GVYAD+ +  GWWDNMVGPGKPLDTN+FFVIGVNNLGSCFGSTGPMSIDPATG PYGA F
Sbjct: 61  GVYADNLKDIGWWDNMVGPGKPLDTNKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGATF 120

Query: 121 PVVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKL 180
           PVVTVEDWV+AQARVAD FGI RFAAVMGGSLGGMQALAWS++YPERV HCI +ASTPKL
Sbjct: 121 PVVTVEDWVNAQARVADQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKL 180

Query: 181 SAQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGR 240
           SAQNIAFNEVARSAILSDPDFHGG+YYAH VKP+RGLRVARMIGHITYLSDDDMAEKFGR
Sbjct: 181 SAQNIAFNEVARSAILSDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGR 240

Query: 241 ALRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNG 300
           +LRRA+GALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAF G
Sbjct: 241 SLRRAEGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFEG 300

Query: 301 NLSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLD 360
           +L+AA+AHT AKYL+ASFTTDWRFAPARSRE+VKALLD++R+V+YAEIDAPHGHDAFLLD
Sbjct: 301 DLTAAVAHTTAKYLIASFTTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLD 360

Query: 361 DARYHNLVRAYYERIAEEVGA 381
           DARYHNL+RAYYERIA EV A
Sbjct: 361 DARYHNLMRAYYERIANEVNA 381


Lambda     K      H
   0.322    0.136    0.417 

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: 641
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: 381
Length of database: 381
Length adjustment: 30
Effective length of query: 351
Effective length of database: 351
Effective search space:   123201
Effective search space used:   123201
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 (21.9 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