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_011383255.1 AMB_RS04150 acetylornithine transaminase

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



>NCBI__GCF_000009985.1:WP_011383255.1
          Length = 388

 Score =  451 bits (1160), Expect = e-131
 Identities = 226/377 (59%), Positives = 278/377 (73%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           ++P + R D++FE+GEG +L A+DGRRFLDF AGVAVN LGHA+P LV AL AQA KLWH
Sbjct: 6   LLPVFDRTDVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWH 65

Query: 65  TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124
            SNL+RV GQE +A+RL +A+FADT FF N+GAEA E   K+ R+YH+  G   R RI+ 
Sbjct: 66  CSNLYRVPGQERVAERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVA 125

Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184
              +FHGRT+A ++AA   K ++GFGP+  GFD VP+GDLEA R A+   TA + +EP+Q
Sbjct: 126 CTGSFHGRTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAIGSNTAALLVEPVQ 185

Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244
           GEGGIR     +LRGLR + D+ GLLL +DE+Q G+GRTGKLFAHEW+GI PDVM +AKG
Sbjct: 186 GEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMGLAKG 245

Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304
           +GGGFP+GA LATEKAAS MT GTHG T+GGNPLA AV  AVLD+V+ PGFL+ VQ +  
Sbjct: 246 LGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAVAA 305

Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364
           LL+ RL  L    P     VRG+GLMLGL   P   +    L A GLL+V AGDNVVRL+
Sbjct: 306 LLRGRLDDLARRYPGAIAQVRGQGLMLGLKTVPVNTEFNAKLFAAGLLAVGAGDNVVRLV 365

Query: 365 PPLNIGEAEVEEAVAIL 381
           PPL IGEAEVE AV I+
Sbjct: 366 PPLIIGEAEVERAVEII 382


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: 497
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: 388
Length adjustment: 30
Effective length of query: 359
Effective length of database: 358
Effective search space:   128522
Effective search space used:   128522
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