GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Pseudomonas simiae WCS417

Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase

Query= SwissProt::Q83A83
         (387 letters)



>FitnessBrowser__WCS417:GFF2301
          Length = 411

 Score =  310 bits (793), Expect = 6e-89
 Identities = 172/397 (43%), Positives = 251/397 (63%), Gaps = 17/397 (4%)

Query: 5   NNKKSHI--DTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSP--------GVHQGYEYSR 54
           NNK +     TR IH G  P    GA++ PIY ++T+A  +         G   G+ Y+R
Sbjct: 2   NNKHNAFGFSTRAIHHGYDPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTR 61

Query: 55  SQNPTRFAYERCVADLESGQHGFAFASGMAA-TATILELLQPGDHVVVMDDVYGGSYRLF 113
             NPT    E  +A LE+G    AF+SGM A  AT   LL+PGD V+V   +YG ++ L 
Sbjct: 62  ISNPTLALLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALL 121

Query: 114 ENVRKRSAGLSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEK- 172
            +      G+    VD TD   ++ A+T  T+M++ E+P+NP L++VD+A +A +A ++ 
Sbjct: 122 HH-GIGEFGIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQP 180

Query: 173 NIIAVADNTFATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKY- 231
           N+  V DNT+ TP +QRPLELG D+V HSATKYL+GH DI  G+AV   N+ LA++++  
Sbjct: 181 NVTLVVDNTYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAV--SNQALAQRIRLQ 238

Query: 232 -LQNAIGAIAAPFDSFMVLRGLKTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSH 290
            L++  GA+ +P D+ +++RGLKTLA+RM+RHC NA  +A+ L+ HP V+ V YPGL S 
Sbjct: 239 GLKDLTGAVMSPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSF 298

Query: 291 PQHSIAKKQMRYFGGMISVELKCDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHA 350
           PQ+ +A +QM+  GGMI+ ELK  +   ++ +   +LFT A SLG  ESL +HPA MTH+
Sbjct: 299 PQYELATQQMKMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHS 358

Query: 351 SIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAAL 387
           +    ER   GI++G +RLSVG+E + DL  D++ AL
Sbjct: 359 TYTPQERAAHGISEGLVRLSVGLEDVADLLADVQQAL 395


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: 417
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 387
Length of database: 411
Length adjustment: 31
Effective length of query: 356
Effective length of database: 380
Effective search space:   135280
Effective search space used:   135280
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