GapMind for Amino acid biosynthesis

 

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

Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate 7025489 Shewana3_2643 methionine gamma-lyase (RefSeq)

Query= BRENDA::Q1M0P5
         (380 letters)



>FitnessBrowser__ANA3:7025489
          Length = 397

 Score =  309 bits (791), Expect = 1e-88
 Identities = 172/386 (44%), Positives = 236/386 (61%), Gaps = 11/386 (2%)

Query: 5   TKLIHGGISEDATTGAVSVPIYQTSTYRQDAI--------GHHKGYEYSRSGNPTRFALE 56
           T+ IH G   +A  G +  P+YQT+T+  ++         G+  GY Y+R GNPT   LE
Sbjct: 13  TQAIHAGHEREAF-GTLVTPLYQTATFVFESAQQGGERFAGNEPGYIYTRLGNPTVAELE 71

Query: 57  ELIADLEGGVKGFAFASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLS 115
             +A LEG     A ASG+  + A + + LQ GDH++  + VYG TF L      + G+ 
Sbjct: 72  RKMAILEGAEAAAATASGMGAVSAALLANLQMGDHLVASNAVYGCTFALMTSQFARFGIE 131

Query: 116 CTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFAT 175
            T++D +DL+ I++AIKPNT+ ++ ETP NP L++ DL   A +AK H L++IVDNTF T
Sbjct: 132 VTLVDFTDLAAIERAIKPNTRVIFCETPVNPHLQVFDLKGIADIAKRHQLVSIVDNTFMT 191

Query: 176 PYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDS 235
           P  Q PL  G D+VVHS TKYL GH DV+AG+V  + E L +        IG V+ P D+
Sbjct: 192 PLLQQPLAFGIDLVVHSATKYLNGHGDVIAGVVCGSEEQLHRVKYEILKDIGAVMSPHDA 251

Query: 236 WLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSG 295
           WL+ RG+KTL +R+Q H  +A  VAEFLE+HP V RVYYPGL +H  +     QM    G
Sbjct: 252 WLILRGLKTLDVRLQRHCDSAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIGGQMAKAGG 311

Query: 296 MLSFTLKNDSE-ATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDG 354
           +++F L    E A  FV  LKLF +  SLG  ESL+  PA MTH+      R+AAGI D 
Sbjct: 312 VIAFELAASLEQAMAFVGYLKLFSIAVSLGDAESLIQHPASMTHSPYTPEARQAAGISDN 371

Query: 355 LVRLSVGIEHEQDLLEDLEQAFAKIS 380
           L+R+S+G+E   D++EDL QA A ++
Sbjct: 372 LLRISIGLEDCGDIIEDLNQALAMLA 397


Lambda     K      H
   0.318    0.136    0.394 

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: 20
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: 380
Length of database: 397
Length adjustment: 30
Effective length of query: 350
Effective length of database: 367
Effective search space:   128450
Effective search space used:   128450
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