GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Cupriavidus basilensis 4G11

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate RR42_RS05540 RR42_RS05540 NADH dehydrogenase

Query= uniprot:Q39TW6
         (218 letters)



>FitnessBrowser__Cup4G11:RR42_RS05540
          Length = 792

 Score =  101 bits (251), Expect = 5e-26
 Identities = 67/205 (32%), Positives = 98/205 (47%), Gaps = 31/205 (15%)

Query: 4   INLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWPKLV 63
           + L+IDGK+V   EG  +++AA+ +G  IP  C+H KL     CR+C VEVE    PK +
Sbjct: 2   VELEIDGKKVEVAEGSLVMEAARQLGTYIPHFCYHRKLSIAANCRMCLVEVEKA--PKAL 59

Query: 64  AGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYGAD 114
             C  PV  G+ V T +EK  K +K ++E +L + P            +L+ LA  YGA 
Sbjct: 60  PACATPVTPGMKVFTNSEKAVKAQKSVMEFLLINHPLDCPICDQGGECQLQDLAVGYGAS 119

Query: 115 RDRFEKHP-----------------SFCIHCGLCVRYCAEIKKKNAVGFVDRGSNREI-S 156
             R+++                   S CIHC  CVR+  E+     +G + RG + EI +
Sbjct: 120 ESRYKEEKRVVFHKNVGPLISMEEMSRCIHCTRCVRFGQEVAGVMELGMLGRGEHSEITT 179

Query: 157 FIPEIAAKECWDCKECFPLCPTSAL 181
           F+ +    E         LCP  AL
Sbjct: 180 FVGQTVDSEL--SGNMIDLCPVGAL 202


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: 310
Number of extensions: 14
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: 792
Length adjustment: 31
Effective length of query: 187
Effective length of database: 761
Effective search space:   142307
Effective search space used:   142307
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