GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Burkholderia phytofirmans PsJN

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate BPHYT_RS15405 BPHYT_RS15405 aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__BFirm:BPHYT_RS15405
          Length = 398

 Score =  201 bits (512), Expect = 2e-56
 Identities = 131/359 (36%), Positives = 195/359 (54%), Gaps = 18/359 (5%)

Query: 29  DVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADF-NYD 87
           D+I + IG+PDF  P  V  AA  A+   VT YT   G   LR+A+  +    ADF   D
Sbjct: 39  DIIHMGIGEPDFTAPEPVIEAAASALRRGVTQYTSALGLHALREAISAHY---ADFYGVD 95

Query: 88  AE-SEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-TSH 145
            + + I++T GAS A+  A   ++   DEV+MP P YP     +     +PV+V +  + 
Sbjct: 96  VDPARIVVTAGASAALLLACAALVDRDDEVLMPDPCYPCNRHFVIAAEGRPVMVPSGPAE 155

Query: 146 GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSE 205
            F+LTA  +E     +T+ V+L  PSNPTG ++   EL+ I   ++ R  F + DEIY  
Sbjct: 156 RFQLTAADVERLWNEHTRGVLLASPSNPTGTSIEPAELERIVKAVRARGGFTIVDEIYQG 215

Query: 206 LTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCAS 265
           L+YD    S  ++  D  I +N  SK  +MTGWR+G+L  P  +     K+ Q    CAS
Sbjct: 216 LSYDAKPVSALSF-GDDVITVNSFSKYFNMTGWRLGWLVVPPGMVSAFEKLAQNLFICAS 274

Query: 266 SISQKAAL---EAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDV-VKPSGAFYIFPSI 321
           +++Q AAL   E  T    +A   R+++K+R D++   L S+G  V V P GAFY++   
Sbjct: 275 ALAQHAALACFEPETIAIYEA--RRQEFKRRRDFIAPALESLGFSVPVMPDGAFYVYADC 332

Query: 322 KSFGMT----SFDFSMALLEDAGVALVPGSSFSTYG-EGYVRLSFACSMDTLREGLDRL 375
           ++   +    S   + A+L DAGV LVPG  F T+  + Y+RLS+A +   L E +DRL
Sbjct: 333 RTVAHSAAGDSAALTKAMLHDAGVVLVPGMDFGTHAPKDYIRLSYATAYPKLEEAVDRL 391


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: 343
Number of extensions: 16
Number of successful extensions: 8
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: 398
Length adjustment: 31
Effective length of query: 362
Effective length of database: 367
Effective search space:   132854
Effective search space used:   132854
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