GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dino:3607384
          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:

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