Alignments for a candidate for cimA in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Xanthobacter autotrophicus Py2

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011995828.1 XAUT_RS00750 homocitrate synthase

Query= curated2:Q8TYM1
         (509 letters)



>NCBI__GCF_000017645.1:WP_011995828.1
          Length = 415

 Score =  275 bits (704), Expect = 2e-78
 Identities = 159/364 (43%), Positives = 209/364 (57%), Gaps = 3/364 (0%)

Query: 18  DTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAREELDA 77
           DTTLRDGEQ PGVA T  EK+ IA  L   GV  IEAG  A  + E++ +R I   +L  
Sbjct: 37  DTTLRDGEQAPGVAFTRREKIEIAEALAAAGVPEIEAGTPAMGDEEIETLRSIVSLKLPL 96

Query: 78  EVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEYARDH 137
            V +  RM + D+ AAV A    V++ +PTS+  +K KL  DR+  L   R VV  A   
Sbjct: 97  RVAAWCRMSEEDLFAAVSAGVTYVNLSIPTSDRQLKGKLNRDRDWALGALRHVVTLATKL 156

Query: 138 GLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLRERVG 197
           G T  +  ED +R + ++L +V +   EAGA RL   DT+GV+ P   +  V+++     
Sbjct: 157 GFTAAVGCEDASRADPDFLCKVAEVAKEAGAFRLRLADTLGVLDPFSAYALVRRVANAT- 215

Query: 198 EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEELYGV 257
            D+ +  H HDD G+ATANT+AAV  GAR   VTV G+GERAGNAALEEV + L +    
Sbjct: 216 -DLEIEFHAHDDLGLATANTLAAVTGGARHASVTVAGLGERAGNAALEEVAIALRQTARS 274

Query: 258 DTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEPIPPE 317
           +TGI    L  L++ V    G  +P  KA+VGE+ FTHESGIH  G+LKD  TYE + PE
Sbjct: 275 ETGIDPHALRPLAQKVMEAAGRPMPRTKAIVGEDIFTHESGIHVSGLLKDRGTYEALSPE 334

Query: 318 KVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRITEAD-LRA 376
            +G   R VLGKH G + I K L   G+ VD+ +   IL R++    R K     D LR 
Sbjct: 335 MLGRSHRVVLGKHSGLAAILKALSDQGLAVDEARGRAILARVRDFAIRSKNSVSPDVLRR 394

Query: 377 IAED 380
             ED
Sbjct: 395 FYED 398


Lambda     K      H
   0.315    0.134    0.367 

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: 479
Number of extensions: 26
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: 509
Length of database: 415
Length adjustment: 33
Effective length of query: 476
Effective length of database: 382
Effective search space:   181832
Effective search space used:   181832
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis