GapMind for Amino acid biosynthesis

 

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

Align Cystathionine beta-lyase MetC; CBL; Beta-cystathionase MetC; Cysteine lyase MetC; Cysteine-S-conjugate beta-lyase MetC; EC 4.4.1.13 (characterized)
to candidate 7025489 Shewana3_2643 methionine gamma-lyase (RefSeq)

Query= SwissProt::O31632
         (390 letters)



>FitnessBrowser__ANA3:7025489
          Length = 397

 Score =  317 bits (813), Expect = 3e-91
 Identities = 171/394 (43%), Positives = 238/394 (60%), Gaps = 11/394 (2%)

Query: 2   SKHNWTLETQLVHNPFKTDGGTGAVSVPIQHASTFHQSSFEEFG--------AYDYSRSG 53
           S   W   TQ +H   + +   G +  P+   +TF   S ++ G         Y Y+R G
Sbjct: 5   SSKQWKAATQAIHAGHEREA-FGTLVTPLYQTATFVFESAQQGGERFAGNEPGYIYTRLG 63

Query: 54  TPTRTALEETIAALEGGTRGFAFSSGMAAISTAFLL-LSQGDHVLVTEDVYGGTFRMVTE 112
            PT   LE  +A LEG     A +SGM A+S A L  L  GDH++ +  VYG TF ++T 
Sbjct: 64  NPTVAELERKMAILEGAEAAAATASGMGAVSAALLANLQMGDHLVASNAVYGCTFALMTS 123

Query: 113 VLTRFGIEHTFVDMTDRNEVARSIKPNTKVIYMETPSNPTLGITDIKAVVQLAKENGCLT 172
              RFGIE T VD TD   + R+IKPNT+VI+ ETP NP L + D+K +  +AK +  ++
Sbjct: 124 QFARFGIEVTLVDFTDLAAIERAIKPNTRVIFCETPVNPHLQVFDLKGIADIAKRHQLVS 183

Query: 173 FLDNTFMTPALQRPLDLGVDIVLHSATKFLSGHSDVLSGLAAVKDEELGKQLYKLQNAFG 232
            +DNTFMTP LQ+PL  G+D+V+HSATK+L+GH DV++G+    +E+L +  Y++    G
Sbjct: 184 IVDNTFMTPLLQQPLAFGIDLVVHSATKYLNGHGDVIAGVVCGSEEQLHRVKYEILKDIG 243

Query: 233 AVLGVQDCWLVLRGLKTLQVRLEKASQTAQRLAEFFQKHPAVKRVYYPGLADHPGAETHK 292
           AV+   D WL+LRGLKTL VRL++   +AQR+AEF ++HPAV RVYYPGL  H G     
Sbjct: 244 AVMSPHDAWLILRGLKTLDVRLQRHCDSAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIG 303

Query: 293 SQSTGAGAVLSFEL-ESKEAVKKLVENVSLPVFAVSLGAVESILSYPATMSHAAMPKEER 351
            Q   AG V++FEL  S E     V  + L   AVSLG  ES++ +PA+M+H+    E R
Sbjct: 304 GQMAKAGGVIAFELAASLEQAMAFVGYLKLFSIAVSLGDAESLIQHPASMTHSPYTPEAR 363

Query: 352 EKRGITDGLLRLSVGVEHADDLEHDFEQALKEIA 385
           +  GI+D LLR+S+G+E   D+  D  QAL  +A
Sbjct: 364 QAAGISDNLLRISIGLEDCGDIIEDLNQALAMLA 397


Lambda     K      H
   0.317    0.132    0.374 

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: 389
Number of extensions: 16
Number of successful extensions: 3
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: 390
Length of database: 397
Length adjustment: 31
Effective length of query: 359
Effective length of database: 366
Effective search space:   131394
Effective search space used:   131394
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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