GapMind for Amino acid biosynthesis

 

Aligments for a candidate for CGL in Dyella japonica UNC79MFTsu3.2

Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate N515DRAFT_2767 N515DRAFT_2767 cysteine synthase A

Query= BRENDA::F4K5T2
         (323 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2767 N515DRAFT_2767 cysteine
           synthase A
          Length = 313

 Score =  235 bits (599), Expect = 1e-66
 Identities = 137/310 (44%), Positives = 197/310 (63%), Gaps = 7/310 (2%)

Query: 6   LIKNDVTELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLI 65
           +I + + + IG TP+V L+++    V  +  K+E   P  S+KDR+A ++I DAE +G I
Sbjct: 1   MIYDSILDTIGKTPVVKLHRLAPKHV-ELYVKVEAFNPAGSVKDRLALAIILDAEARGTI 59

Query: 66  TPGKSTLIEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEVHLTDISI 125
            PG+ T++EAT GNTG+ LA++ A+RGY  + +M  T S+ERR ++RA G +V LT  + 
Sbjct: 60  KPGQ-TVVEATSGNTGVALAAVCAARGYPFVAVMTETFSIERRKLIRAYGGKVLLTPAAE 118

Query: 126 GIKGQLEKAKEILSKTPGGYIPHQFINPENPEIHYRTTGPEIWRDSAGK-VDILVAGVGT 184
              G + KAKE+  K  G ++  QF NP NP  H  TT  EI RD AG+ +D  V G GT
Sbjct: 119 RGSGMVRKAKELADKH-GWFLARQFENPANPAYHRSTTAAEILRDFAGRRLDYFVTGWGT 177

Query: 185 GGTVTGTGKFLKEKNKDIKVCVVEPSESAVLSGGKPGPHLIQGIGSGEIPANLDLSIVDE 244
           GGT+TG G+ LK    ++KV   EP+ +++L+G +  PH IQG     +PA L+  +  +
Sbjct: 178 GGTLTGVGEVLKVARPEVKVIASEPAGASLLAGKEWQPHKIQGWTPDFVPAVLNREVAQQ 237

Query: 245 IIQVTGEEAIETTKLLAIKEGLLVGISSGASAAAALKVAK-RPENVGKLIVVIFPSGGER 303
           I+ V    A +T++ LA KEG+ VGISSGA+ AAAL+VAK  PE  G +++ + P  GER
Sbjct: 238 ILPVDDVVARDTSRALAQKEGIFVGISSGATLAAALQVAKDAPE--GSVLLAMLPDTGER 295

Query: 304 YLSTELFESV 313
           YLST LFE V
Sbjct: 296 YLSTFLFEGV 305


Lambda     K      H
   0.314    0.136    0.378 

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: 236
Number of extensions: 11
Number of successful extensions: 6
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: 323
Length of database: 313
Length adjustment: 27
Effective length of query: 296
Effective length of database: 286
Effective search space:    84656
Effective search space used:    84656
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: 42 (21.9 bits)
S2: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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