GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Methylocapsa aurea KYG

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate WP_036257391.1 DL86_RS01350 formate dehydrogenase subunit alpha

Query= uniprot:Q39TW6
         (218 letters)



>NCBI__GCF_000746085.1:WP_036257391.1
          Length = 948

 Score =  101 bits (251), Expect = 5e-26
 Identities = 75/236 (31%), Positives = 107/236 (45%), Gaps = 34/236 (14%)

Query: 4   INLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVR-GWPKL 62
           + L IDG EV A EG +I+ AA  +G  IP LC  + LE +G CR+C VE++ R G P  
Sbjct: 20  VTLTIDGVEVHAPEGTSIMRAAMEIGTQIPKLCASDMLEAFGSCRLCLVEIQGRNGTP-- 77

Query: 63  VAGCIYPVEKGLVVRTRNEKIDKIRKVLLE--------EMLAHAPDSE-ELKALAQEYGA 113
            A C  PV  G+VV+T+ E++  +RK ++E        + L  A +S+ EL+  A   G 
Sbjct: 78  -ASCTTPVAPGMVVKTQTERLKALRKGVMELYISDHPLDCLTCAANSDCELQTQAGAVGL 136

Query: 114 DRDRF-------------EKHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNRE 154
              R+             E +P F      CI C  CVR C E++   A+    RG    
Sbjct: 137 REVRYGYDGANHFAEKKDESNPYFTYDPAKCIVCNRCVRACEEVQGTFALTIDGRGFESR 196

Query: 155 ISFIPE--IAAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEAHSGGCGCSCS 208
           ++   +      EC  C  C   CPT+ L    V+A              CG  C+
Sbjct: 197 VAPGQDEPFFESECVSCGACVQACPTATLTEKSVIAIGQPEHSAVTTCAYCGVGCT 252


Lambda     K      H
   0.320    0.137    0.432 

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: 480
Number of extensions: 25
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: 218
Length of database: 948
Length adjustment: 32
Effective length of query: 186
Effective length of database: 916
Effective search space:   170376
Effective search space used:   170376
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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