GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Shewanella sp. ANA-3

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 7025489 Shewana3_2643 methionine gamma-lyase (RefSeq)

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



>FitnessBrowser__ANA3:7025489
          Length = 397

 Score =  339 bits (869), Expect = 1e-97
 Identities = 178/393 (45%), Positives = 248/393 (63%), Gaps = 3/393 (0%)

Query: 7   QDRSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYS 66
           QD S  Q WK ATQAI  G  R  +G     L+ T+ + ++ A     RF+G++ G  Y+
Sbjct: 2   QDESSKQ-WKAATQAIHAGHEREAFGTLVTPLYQTATFVFESAQQGGERFAGNEPGYIYT 60

Query: 67  RLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWL 126
           RL NPTV  LE+++A+LEGAEA  ATASGM A++AALL  L  GDHL+   A +G    L
Sbjct: 61  RLGNPTVAELERKMAILEGAEAAAATASGMGAVSAALLANLQMGDHLVASNAVYGCTFAL 120

Query: 127 TDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERG 186
             +Q  +FGIE T+VD  D      AI+PNT+V F ETP NP + V DLK +  IA+   
Sbjct: 121 MTSQFARFGIEVTLVDFTDLAAIERAIKPNTRVIFCETPVNPHLQVFDLKGIADIAKRHQ 180

Query: 187 IVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHR 246
           +V++VDN F TP LQ+P+ FG D+V +SATK ++G G V+AG VCG+EE ++       +
Sbjct: 181 LVSIVDNTFMTPLLQQPLAFGIDLVVHSATKYLNGHGDVIAGVVCGSEEQLHRVKYEILK 240

Query: 247 NTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHN 304
           + G  +SP +AW++L+GL+TLD+R+QR  ++A +VA FLE    V RV +PGL SH  H 
Sbjct: 241 DIGAVMSPHDAWLILRGLKTLDVRLQRHCDSAQRVAEFLEQHPAVTRVYYPGLKSHSGHR 300

Query: 305 LAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAE 364
               QMA AG + + EL     QA   +  L L  I+ ++GD+ SL+ HPAS THS    
Sbjct: 301 FIGGQMAKAGGVIAFELAASLEQAMAFVGYLKLFSIAVSLGDAESLIQHPASMTHSPYTP 360

Query: 365 DQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397
           + R   G+ + +LR+++GLED  D+I DL+QAL
Sbjct: 361 EARQAAGISDNLLRISIGLEDCGDIIEDLNQAL 393


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: 353
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: 397
Length adjustment: 31
Effective length of query: 371
Effective length of database: 366
Effective search space:   135786
Effective search space used:   135786
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