GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Pseudomonas fluorescens FW300-N1B4

Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)

Query= SwissProt::Q83A83
         (387 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890
          Length = 393

 Score =  512 bits (1318), Expect = e-150
 Identities = 249/375 (66%), Positives = 298/375 (79%)

Query: 13  TRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGVHQGYEYSRSQNPTRFAYERCVADLES 72
           TRVIHAGQ PDP TGA+M PIY  STY Q+SPGVH+G++Y RS NPTRFA ERCVADLE 
Sbjct: 15  TRVIHAGQTPDPSTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNPTRFALERCVADLEG 74

Query: 73  GQHGFAFASGMAATATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAGLSFSFVDFTD 132
           G   FAFASG+AA A +LELL  G H+V  +D+YGG++RLF+ VR+RSAG  FSFVD TD
Sbjct: 75  GTRAFAFASGLAAIANVLELLDAGAHIVSGNDLYGGTFRLFDKVRRRSAGHRFSFVDLTD 134

Query: 133 ENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTFATPIIQRPLE 192
                 A+   T+M+WVE+PSNP L + DL  +A I +++ II VADNTFA+P IQRPLE
Sbjct: 135 LAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIICVADNTFASPWIQRPLE 194

Query: 193 LGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKYLQNAIGAIAAPFDSFMVLRGL 252
           LGFDIV HS TKYLNGHSD+IGG+AVVG N  LAE+L +LQNA+GAIA PFD+F+ LRG+
Sbjct: 195 LGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELAERLGFLQNAVGAIAGPFDAFLTLRGV 254

Query: 253 KTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVELK 312
           KTLA+RMERHC NA++LAQWLE+ P+V RVYYPGLPSHPQH +A++QMR FGGMIS++L 
Sbjct: 255 KTLALRMERHCSNALELAQWLERQPQVARVYYPGLPSHPQHELARRQMRGFGGMISLDLN 314

Query: 313 CDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVG 372
            DL   K+ LE  ++F LAESLGGVESLIEHPAIMTHASIP   R +LGI D  +RLSVG
Sbjct: 315 SDLAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRAQLGIGDALVRLSVG 374

Query: 373 IEAITDLRHDLEAAL 387
           +E + DLR DL  AL
Sbjct: 375 VEDVEDLRADLAQAL 389


Lambda     K      H
   0.319    0.134    0.385 

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: 483
Number of extensions: 13
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: 387
Length of database: 393
Length adjustment: 31
Effective length of query: 356
Effective length of database: 362
Effective search space:   128872
Effective search space used:   128872
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