GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Magnetospirillum magneticum AMB-1

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

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



>NCBI__GCF_000009985.1:WP_083763404.1
          Length = 384

 Score =  475 bits (1223), Expect = e-139
 Identities = 238/383 (62%), Positives = 290/383 (75%)

Query: 6   MPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHT 65
           MPTYARAD+ FERGEG YL+  DGRR+LDFAAGVAVN LGH +P LV+ALTAQA K+WHT
Sbjct: 1   MPTYARADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHT 60

Query: 66  SNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITF 125
           SNL+RVAGQES+A +L E +FADTVFF NSGAEA EC  K+ R++H+  G+  R RII  
Sbjct: 61  SNLYRVAGQESVAAKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICA 120

Query: 126 EQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQG 185
           E AFHGRTLA V+A  Q+K ++GF P +DGFD VP+G+L A+R ++T+ETA I +EP+QG
Sbjct: 121 EGAFHGRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALRASITEETAAILVEPVQG 180

Query: 186 EGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGI 245
           EGGI  G  ++LR LR   DE GLLL  DE+Q GMGRTG LFAHE AGI PD+M VAKG+
Sbjct: 181 EGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAGIAPDIMGVAKGL 240

Query: 246 GGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305
           GGGFP+GACLAT KAASGM  GTHGST+GGNPLA AV   VLD + EPGFL+HVQ +  L
Sbjct: 241 GGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEPGFLEHVQAMAAL 300

Query: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLP 365
           L+ ++    A  P V + VRG GLMLG+       ++V  L   GLL+V AGDN+VRLLP
Sbjct: 301 LRSKVEDTAARFPGVVEEVRGLGLMLGIKPRMPNTEMVARLAEGGLLTVGAGDNIVRLLP 360

Query: 366 PLNIGEAEVEEAVAILAKTAKEL 388
           PL I +A+V+EAV ILA+   E+
Sbjct: 361 PLIINDAQVDEAVGILARAFDEV 383


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: 504
Number of extensions: 21
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: 384
Length adjustment: 30
Effective length of query: 359
Effective length of database: 354
Effective search space:   127086
Effective search space used:   127086
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