GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Phaeobacter inhibens BS107

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD

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



>FitnessBrowser__Phaeo:GFF2392
          Length = 394

 Score =  474 bits (1219), Expect = e-138
 Identities = 238/385 (61%), Positives = 288/385 (74%)

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

Query: 61  KLWHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKART 120
            LWH SNL+ +  Q++LA RL E +FADTVFFTNSG E+ E   K+ RKY ++KG   R 
Sbjct: 61  TLWHVSNLYHIPQQQALADRLVEHSFADTVFFTNSGTESCELAVKMARKYFHDKGQPERV 120

Query: 121 RIITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICL 180
            I+TF  +FHGR+ A +SAA  EK+  GFGP+L GF  + FGDL+ V +A+TD+TA I +
Sbjct: 121 EILTFSGSFHGRSSAGISAAGSEKMTAGFGPMLPGFKHLMFGDLDGVTDAITDQTAAILI 180

Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240
           EP+QGEGGIR      L+ LR+ICDEHGLLL LDE+QCG+GRTGKLFAHEWAGITPD+M 
Sbjct: 181 EPVQGEGGIRPVPDAELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMM 240

Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300
           VAKGIGGGFPLGA LATE+AASGMTAGTHGSTYGGNPL  AVG AV+D V +P FL  V 
Sbjct: 241 VAKGIGGGFPLGAVLATEEAASGMTAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVS 300

Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360
           R  GLL+ +L GLVA +P VF+ VRG GLMLGL C  A  DVV A     +++VPA DNV
Sbjct: 301 RKAGLLRQKLEGLVASHPQVFEAVRGSGLMLGLKCVAANTDVVAAGYEAEVVTVPAADNV 360

Query: 361 VRLLPPLNIGEAEVEEAVAILAKTA 385
           VRLLPPL + + ++ EA A L + A
Sbjct: 361 VRLLPPLTLTDEDIAEAFARLDQAA 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: 496
Number of extensions: 20
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: 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