GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Magnetospirillum magneticum AMB-1

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate WP_011385159.1 AMB_RS13980 NADH-quinone oxidoreductase subunit G

Query= uniprot:Q39TW6
         (218 letters)



>NCBI__GCF_000009985.1:WP_011385159.1
          Length = 690

 Score = 98.6 bits (244), Expect = 3e-25
 Identities = 66/202 (32%), Positives = 98/202 (48%), Gaps = 30/202 (14%)

Query: 6   LQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWPKLVAG 65
           L IDG+E+    G TI+ AA  +GI IP  C+HE+L   G CR+C VEVE    PK  A 
Sbjct: 4   LTIDGREIEVEAGTTIIQAADLLGIEIPRFCYHERLAIAGNCRMCLVEVE--KMPKPAAS 61

Query: 66  CIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYGADRD 116
           C  PV +G+VV+T    + K R+ ++E +L + P            +L+  A  YG+D++
Sbjct: 62  CAMPVGEGMVVKTNTPAVRKARQGVMEFLLLNHPLDCPICDQGGECDLQDQAMAYGSDKN 121

Query: 117 RFEKHP----------------SFCIHCGLCVRYCAEIKKKNAVGFVDRGSNREIS-FIP 159
           R ++                  + CI C  CVR+ +EI     +G + RG + EI  ++ 
Sbjct: 122 RCKEGKRAVPDKDYGPLVQTMMTRCIQCTRCVRFISEIAGTPVLGGLGRGEHLEIGRYVG 181

Query: 160 EIAAKECWDCKECFPLCPTSAL 181
              + E         LCP  AL
Sbjct: 182 AAVSSEL--SGNLIDLCPVGAL 201


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: 325
Number of extensions: 15
Number of successful extensions: 3
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: 690
Length adjustment: 30
Effective length of query: 188
Effective length of database: 660
Effective search space:   124080
Effective search space used:   124080
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. 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