GapMind for Amino acid biosynthesis

 

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

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme

Query= reanno::azobra:AZOBR_RS19025
         (389 letters)



>FitnessBrowser__Burk376:H281DRAFT_04057
          Length = 394

 Score =  277 bits (708), Expect = 4e-79
 Identities = 159/375 (42%), Positives = 226/375 (60%), Gaps = 8/375 (2%)

Query: 11  RADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFR 70
           R +IVF  G+G +LY  +G+R+LDF  G AVN LGH +  ++EAL  QA  L++ S  F 
Sbjct: 17  RPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPSPAFY 76

Query: 71  VAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAFH 130
                 LA  LT+ +  D VFF NSGAEA E   KL RK+  +  D A   IITF+ +FH
Sbjct: 77  NEPMAKLAALLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFKDGA-FEIITFDHSFH 135

Query: 131 GRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEGGIR 190
           GRTLA +SA+ +      + P + GF      D+ +V   +  +T  + LEPIQGEGG+ 
Sbjct: 136 GRTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVI 195

Query: 191 AGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGGGFP 250
             + EF++ LRE+  +H +LL +DE+Q G GR G LFA+E +G+ PD+M + KGIGGG P
Sbjct: 196 PATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMTLGKGIGGGVP 255

Query: 251 LGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQDRL 310
           L A LA  + A    AG  G TY GNPL TAVG +V+ ++  PGFL+ V+  G  L+ +L
Sbjct: 256 LAALLAKAEVAV-FEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGVRARGEYLRAKL 314

Query: 311 AGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVA----LRANGLLSVPAGDNVVRLLPP 366
             L  E    FKG RG+GL+  L  G  +G+ +V     ++ +GLL   A  N++R +P 
Sbjct: 315 LELSEERG--FKGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPA 372

Query: 367 LNIGEAEVEEAVAIL 381
           LN+   E+++ +A+L
Sbjct: 373 LNVTNEEIDQMMAML 387


Lambda     K      H
   0.321    0.139    0.414 

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: 405
Number of extensions: 23
Number of successful extensions: 5
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: 389
Length of database: 394
Length adjustment: 31
Effective length of query: 358
Effective length of database: 363
Effective search space:   129954
Effective search space used:   129954
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 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