GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Xanthobacter autotrophicus Py2

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_011996059.1 XAUT_RS02030 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P16524
         (393 letters)



>NCBI__GCF_000017645.1:WP_011996059.1
          Length = 395

 Score =  212 bits (539), Expect = 2e-59
 Identities = 130/369 (35%), Positives = 202/369 (54%), Gaps = 8/369 (2%)

Query: 23  LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82
           L  Q   +++L IGQPDF TP H+  AA KA+ +    YTP+ G L LR+AV   + ++ 
Sbjct: 26  LAGQGRSILNLGIGQPDFRTPDHIVEAAVKALRDGQHGYTPSVGILPLREAVAADLNRRY 85

Query: 83  DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVD- 141
               D +  ++I  G    + AA R    PG E++ P P +P Y  +I   GA PV V  
Sbjct: 86  GVEVDPDL-VMIMPGGKVTMYAAIRLFGEPGAEILYPDPGFPIYRSMIEHTGATPVPVPI 144

Query: 142 TTSHGFKLTARLIEDALTPNTKCVVLPYPSNPT-GVTLSEEELKSIAALLKGRNVFVLSD 200
              +GF  +A      +TP T+ +++  P+NPT GVT + E  K +  L    +V ++SD
Sbjct: 145 REENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPAAEIDKLVKGLAAHPHVALMSD 204

Query: 201 EIYSELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVH 257
           EIY    +D   H ++  Y  +RD+ I++NG SK+++MTGWR+G+   PKD+   + K+ 
Sbjct: 205 EIYDRFLFDGEEHRTLLAYPQIRDRLILLNGWSKTYAMTGWRLGYSIWPKDLYDKVRKLA 264

Query: 258 QYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFY 316
               SC ++ +Q A + A+    D    M  ++  R   V D L ++ G+    P GAFY
Sbjct: 265 VNCWSCVNAATQYAGIAALEGPQDAVDAMTAEFDARRRIVVDGLNALPGVRCATPKGAFY 324

Query: 317 IFPSIKSFGMT-SFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRL 375
            FP++   G + +   + ALLE+AGVA++ G  F  YGEGY+RLS+A S + +   L R+
Sbjct: 325 AFPNVSGTGWSEAKKLASALLEEAGVAVIGGPDFGVYGEGYLRLSYATSRENIAAALARM 384

Query: 376 ELFVLKKRE 384
             F+   R+
Sbjct: 385 GDFLAANRK 393


Lambda     K      H
   0.319    0.135    0.388 

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: 400
Number of extensions: 25
Number of successful extensions: 7
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: 393
Length of database: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
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 Jul 25 2024. The underlying query database was built on Jul 25 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