GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Phaeobacter inhibens BS107

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate GFF1638 PGA1_c16600 methionine gamma-lyase MdeA

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>FitnessBrowser__Phaeo:GFF1638
          Length = 401

 Score =  301 bits (772), Expect = 2e-86
 Identities = 164/386 (42%), Positives = 244/386 (63%), Gaps = 4/386 (1%)

Query: 18  ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76
           +T+AI  G   +S+ G  +  L+LTS + +D A      F+G+++G  YSR+ NPT++ L
Sbjct: 9   STRAIHHGYDTQSQQGSLNPPLYLTSTFTFDSAEAGGEMFTGEREGHFYSRISNPTLDHL 68

Query: 77  EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136
           EQRIA LEG EA  ATASGM A+T+ L   L+AGD +I  +  +G         LP+FG+
Sbjct: 69  EQRIANLEGGEAGLATASGMGAITSTLWSFLAAGDEIILDKTLYGCTFSFMTHGLPRFGV 128

Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196
           +  +VD  DP    +AI P TK+ +FETPANP   ++D+ A+  IA + G   VVDN FA
Sbjct: 129 KVRLVDMTDPTNLAEAISPKTKLVYFETPANPNNRLIDIAAISEIAHKAGAKVVVDNTFA 188

Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINN-TLLPFHRNTGPTLSPF 255
           TP L RP++ GAD+V +SATK + G G V+AG V G++E I    L+     TG  +SPF
Sbjct: 189 TPVLTRPIELGADIVVHSATKFISGHGDVIAGLVVGSKEEITQIRLVGLKDMTGAVMSPF 248

Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAA 313
           +A ++++GL+TL+LR++R  ++ALKVA  L+    V RV +PGL    Q +LA  QM+  
Sbjct: 249 SAMLLMRGLKTLELRMERHCKSALKVAEALQAHPAVERVYYPGLDDFAQGDLARRQMSGF 308

Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373
           G +   E+ GG+     +++ L +I  + ++GD+ +L+ HPAS THS    ++R   G+ 
Sbjct: 309 GGMIPFEVVGGKAGGIAMMNRLAMIQRAVSLGDAETLIQHPASMTHSTYTPEERAEHGIA 368

Query: 374 EGMLRLNVGLEDPEDLIADLDQALGS 399
           EG++R++VGLE  +D+I DL QAL S
Sbjct: 369 EGLVRMSVGLEGVDDIIDDLMQALSS 394


Lambda     K      H
   0.319    0.134    0.396 

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: 406
Number of extensions: 16
Number of successful extensions: 4
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: 402
Length of database: 401
Length adjustment: 31
Effective length of query: 371
Effective length of database: 370
Effective search space:   137270
Effective search space used:   137270
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