GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Epibacterium ulvae U95

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_157843930.1 CV091_RS00350 cystathionine beta-lyase

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



>NCBI__GCF_002796795.1:WP_157843930.1
          Length = 391

 Score =  150 bits (378), Expect = 8e-41
 Identities = 115/367 (31%), Positives = 176/367 (47%), Gaps = 21/367 (5%)

Query: 40  LTSGYAYDCAGD-AAARFSGDQQG-MTYSRLQNPTVEMLEQRIALLEGAEACRATASGMA 97
           L S   +D  G   AAR +  + G + Y R  N     LEQ IA LEGA+A   T+SG+A
Sbjct: 32  LGSTMVFDTLGAFEAARDARYESGTLYYGRYGNSATTKLEQAIARLEGADAVTLTSSGVA 91

Query: 98  AMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNT 157
           A+T +L+     G H++     +G+ R   D  L + G+E +  D        D IRPNT
Sbjct: 92  AITTSLMTFTKPGAHVLVADHVYGNTRTFCDGLLTRQGVEISYFDPLIGSGITDLIRPNT 151

Query: 158 KVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATK 217
               FE P + T +V D+ A+   A+  G+VT++DN ++TP   +P+  G DVV YS +K
Sbjct: 152 VAIMFEAPGSGTFEVPDIPAIAMAAKAAGVVTILDNTWSTPLFCQPLSLGVDVVVYSGSK 211

Query: 218 MMDGQGRVLAGAVCGTEEF---INNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQ 274
            + G    + G    T +    I  T++     TG         + L+GL TL +R++  
Sbjct: 212 YLSGHSDCMLGVTATTLKHHMAIRQTIMQIGDKTGGQ----EIMLALRGLRTLKVRMEYF 267

Query: 275 SENALKVAR-FLE-GRVPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGGRT-QAHGL 331
                ++A+ FLE   V  +  P   + P H       + A  +FS+ L    T +    
Sbjct: 268 DRVGREMAQWFLERPEVKTILHPAFETCPGHANWKRDFSGAASLFSVILKPCDTIRMRAF 327

Query: 332 LDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEG-MLRLNVGLEDPEDLI 390
           ++AL    I  + G   SL+  P     +  A ++       EG ++R N+G+EDPE L 
Sbjct: 328 VNALHHFGIGVSWGGYESLVL-PVEPVRTATAWEE-------EGHLIRFNIGMEDPESLK 379

Query: 391 ADLDQAL 397
           ADL QA+
Sbjct: 380 ADLAQAM 386


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: 305
Number of extensions: 11
Number of successful extensions: 2
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: 391
Length adjustment: 31
Effective length of query: 371
Effective length of database: 360
Effective search space:   133560
Effective search space used:   133560
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 Jul 26 2024. The underlying query database was built on Jul 25 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