GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metY in Echinicola vietnamensis KMM 6221, DSM 17526

Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_1734 Echvi_1734 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= SwissProt::O31631
         (373 letters)



>lcl|FitnessBrowser__Cola:Echvi_1734 Echvi_1734 Cystathionine
           beta-lyases/cystathionine gamma-synthases
          Length = 369

 Score =  232 bits (591), Expect = 1e-65
 Identities = 142/379 (37%), Positives = 204/379 (53%), Gaps = 33/379 (8%)

Query: 6   ETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLE 65
           ET     G +       V  PI LST + H          Y R++NP R  +E+ +A LE
Sbjct: 4   ETLAIHGGEKKSAPHRAVVQPITLSTTFEHH----EESLIYSRSQNPNRMALEELLAQLE 59

Query: 66  NGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWK-KYGLTFHYDDFS 124
            G+   AFSSG AA   +      G  ++  SD+Y G  +     +K K  +TF   D S
Sbjct: 60  KGSAAAAFSSGNAAGMAVFQALPLGSHIVAPSDMYHGLKKQLVELFKDKLEVTF--TDLS 117

Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184
           D + L   I PNTK +++ETP+NP+++ +DI  + ++ KE  + ++ DNTF TPV Q PL
Sbjct: 118 DPENLEKAIQPNTKLLWIETPSNPMLKISDIRRLTKMAKEDDIRVVCDNTFATPVFQNPL 177

Query: 185 ELGADIVIHSATKYLGGHNDLLAG-LVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243
           ELGAD+V+HSATKY GGH+D+L G L+  K +   +++   Q   GAVL PFD +LL+R 
Sbjct: 178 ELGADLVMHSATKYFGGHSDILGGALITKKSDEFWKQIVNVQQTGGAVLSPFDCYLLVRS 237

Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRL 287
           +KTL+ RMR H  +A  +A FL++  ++  V YPG                 GG+LSF +
Sbjct: 238 IKTLAYRMRGHAEHAGMIATFLDQHPKVERVFYPGLTAHPGHDVAKSQMTGFGGILSFLV 297

Query: 288 Q-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSV 346
           + K E  +  + +LK    A SLGGVES I   A     D              L+R SV
Sbjct: 298 KGKPEDADKLISSLKYYTNATSLGGVESLIERRAAVEGPDTKTP--------QNLIRLSV 349

Query: 347 GIEHAEDLKEDLKQALCQV 365
           G+EH +DL ED+++A   +
Sbjct: 350 GLEHLDDLLEDMEKAFYSI 368


Lambda     K      H
   0.319    0.135    0.392 

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: 394
Number of extensions: 27
Number of successful extensions: 5
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: 373
Length of database: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
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 (21.7 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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