GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Dinoroseobacter shibae DFL-12

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)

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



>lcl|FitnessBrowser__Dino:3607384 Dshi_0798 acetylornithine and
           succinylornithine aminotransferase (RefSeq)
          Length = 393

 Score =  465 bits (1197), Expect = e-136
 Identities = 232/385 (60%), Positives = 286/385 (74%)

Query: 1   VIPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAH 60
           +IP ++PTY RA + F +GEG +L   DGRRFLD  AG+AVN LGHA+P LV ALT QA 
Sbjct: 1   MIPAILPTYNRAPLSFVKGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQ 60

Query: 61  KLWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKART 120
            LWH SNL+++  Q+ LA+ L   TFADTVFFTNSG E+ E   K++RK+ ++ G   R 
Sbjct: 61  ALWHVSNLYQIPAQQKLAEMLVAETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERV 120

Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICL 180
            I+TFE +FHGR+ A ++AA  EK+ KGFGPLL GF  +PFG+ EA+++AV D TA I +
Sbjct: 121 EILTFEGSFHGRSSAGIAAAGSEKMTKGFGPLLPGFRHLPFGNHEALQSAVNDRTAAIMV 180

Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240
           EP+QGEGGIRA     L+GLR++CD+HG+L+ LDE+QCG+GRTG+LFAHEWAG++PD+M 
Sbjct: 181 EPVQGEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGVSPDIMM 240

Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300
           VAKGIGGGFPLGA LAT  AASGMTAGTHGSTYGGNPL  AVG AVL+ V   GFL+ V+
Sbjct: 241 VAKGIGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADGFLEEVR 300

Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360
           R  GL++  L GLVAE P VF  VRG GLMLGL C     DVV A     +L VPA +NV
Sbjct: 301 RKAGLMRQALEGLVAEFPGVFAEVRGAGLMLGLVCRAPNTDVVQAGYGAEVLVVPAAENV 360

Query: 361 VRLLPPLNIGEAEVEEAVAILAKTA 385
           VRLLPPL I +AE+ EA+A L K A
Sbjct: 361 VRLLPPLTITDAEIREALARLRKAA 385


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: 500
Number of extensions: 23
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: 389
Length of database: 393
Length adjustment: 31
Effective length of query: 358
Effective length of database: 362
Effective search space:   129596
Effective search space used:   129596
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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