GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Acidovorax sp. GW101-3H11

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Ac3H11_1602 Aspartate aminotransferase (EC 2.6.1.1)

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1602
          Length = 408

 Score =  201 bits (511), Expect = 3e-56
 Identities = 131/373 (35%), Positives = 202/373 (54%), Gaps = 20/373 (5%)

Query: 21  SNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKK 80
           + L  Q + VI L +G+PDF TP H+  AA++A+    T YT   G  EL+ A+Q   K 
Sbjct: 32  NQLKRQGQPVIVLGLGEPDFDTPAHILEAAQQAMARGETHYTVLDGTAELKAAIQHKFKH 91

Query: 81  KADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIV 140
               ++   +EI    GA Q +  A    ++PGDEVI+P P +  Y  ++ + G  PV+V
Sbjct: 92  YNGLDFQL-NEITAGAGAKQILYNALMASVNPGDEVILPAPYWTSYADMVLIAGGVPVVV 150

Query: 141 DTT-SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NVFVL 198
             T ++GF++T   +E A+TP T+ V +  PSNP+G   S E+L+ +  +++    V++L
Sbjct: 151 PCTEANGFRITPEQLEAAITPRTRWVFINSPSNPSGAAYSAEQLRPVLEVVERHPQVWLL 210

Query: 199 SDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHIL 254
           +D+IY  + YD   ++    +   LRD+T+ +NG+SK+++MTGWR+G+   PK +   + 
Sbjct: 211 ADDIYEHILYDGRAFATPAAVLPSLRDRTLTVNGVSKAYAMTGWRLGYGAGPKALIAAMA 270

Query: 255 KVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSG 313
            V     SC SSISQ AA+ A+T   D      + ++ R D V   L VS GL    P G
Sbjct: 271 VVQSQATSCPSSISQAAAVAALTGPQDVVRERCQAFQDRRDLVVAALNVSPGLRCRVPEG 330

Query: 314 AFYIFPSIK-SFGMTS---------FDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFAC 363
           AFY F S + + G T+          DF   LL +  VA+VPG         Y R+S+A 
Sbjct: 331 AFYTFASCEGALGRTTPGGLLLRTDADFCAYLLREHHVAVVPGGVLGL--APYFRISYAA 388

Query: 364 SMDTLREGLDRLE 376
           S   L+E   R++
Sbjct: 389 STADLQEACARIQ 401


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: 353
Number of extensions: 16
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: 408
Length adjustment: 31
Effective length of query: 362
Effective length of database: 377
Effective search space:   136474
Effective search space used:   136474
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