GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Sphingomonas koreensis DSMZ 15582

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase

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



>FitnessBrowser__Korea:Ga0059261_4131
          Length = 398

 Score =  360 bits (925), Expect = e-104
 Identities = 192/375 (51%), Positives = 241/375 (64%), Gaps = 3/375 (0%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRR-FLDFAAGVAVNVLGHANPYLVEALTAQAHKLW 63
           +M  YARA I F+RGEG +LY  DG   +LD  AGVA N LGH +P LV AL AQA KLW
Sbjct: 5   LMNVYARAPIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLW 64

Query: 64  HTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123
           H SN+F + GQ +LA+RLT A+FADTVFFTNSG EA EC  K+ R+YH  +G+  R  +I
Sbjct: 65  HISNMFEMPGQNALAERLTTASFADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVI 124

Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDE-TAGICLEP 182
            F  AFHGRT  A++AA     + GFG  L GF      +  A+  A+ D  TA + +EP
Sbjct: 125 GFSGAFHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSATAAVVVEP 184

Query: 183 IQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEW-AGITPDVMAV 241
           +QGEGG RA +  FL  LR  C  HG+LL  DE+Q GMGRTGKLFAH+W    TPD+MA+
Sbjct: 185 VQGEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMAL 244

Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301
           AK +G GFP+GACLAT +AASGM  G HG+T GGNPLA AV  A  D++ +P  L H + 
Sbjct: 245 AKALGSGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHARE 304

Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVV 361
           +   L+  L  L A +P V   +RGKGL++G+   P     + A R   LL    GDN V
Sbjct: 305 VAQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPNNRAFMAAAREQRLLVAGGGDNCV 364

Query: 362 RLLPPLNIGEAEVEE 376
           RLLPPL +  AE ++
Sbjct: 365 RLLPPLTLTVAEADQ 379


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: 464
Number of extensions: 16
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 358
Effective length of database: 367
Effective search space:   131386
Effective search space used:   131386
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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