GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hcrB in Magnetospirillum magneticum AMB-1

Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate WP_011384424.1 AMB_RS10205 4-hydroxybenzoyl-CoA reductase subunit beta

Query= SwissProt::O33820
         (324 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384424.1 AMB_RS10205
           4-hydroxybenzoyl-CoA reductase subunit beta
          Length = 324

 Score =  483 bits (1244), Expect = e-141
 Identities = 237/324 (73%), Positives = 268/324 (82%)

Query: 1   MNILTDFRTHRPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLA 60
           MNIL DFRT RPA+L+DAV ALA     PL  GTDLLPNLRRGLG P  LVDLTGI G A
Sbjct: 1   MNILPDFRTLRPASLSDAVAALAVPGAEPLAGGTDLLPNLRRGLGKPETLVDLTGITGFA 60

Query: 61  TISTLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDT 120
            IS  ADG+LRIGAGATLEA+AE   +  +WP LAQAA  VAGP+HRAAATLGGNLCQDT
Sbjct: 61  AISVGADGTLRIGAGATLEAVAEDARVLASWPVLAQAASLVAGPSHRAAATLGGNLCQDT 120

Query: 121 RCTFYNQSEWWRSGNGYCLKYKGDKCHVIVKSDRCYATYHGDVAPALMVLDARAEIVGPA 180
           RC FYNQSEWWRSGNG+CLKY+GDKCHV+VKSDRCYATYHGDVAPALMVL+A AE+VGP 
Sbjct: 121 RCVFYNQSEWWRSGNGFCLKYEGDKCHVVVKSDRCYATYHGDVAPALMVLNASAEVVGPK 180

Query: 181 GKRTVPVAQLFRESGAEHLTLEKGELLAAIEVPPTGAWSAAYSKVRIRDAVDFPLAGVAA 240
           G R VPVA LF ESGA HL+L+ GE+LAA+ VPP   W+AAYSKVR+RDA+DFPLAGVA 
Sbjct: 181 GVRLVPVADLFVESGAAHLSLDHGEVLAALLVPPATGWTAAYSKVRVRDAIDFPLAGVAV 240

Query: 241 ALQRDGDRIAGLRVAITGSNSAPLMVPVDALLGGNWDDAAAETLAQLVRKTSNVLRTTIT 300
           AL+RDG+ IAGLRVA+TG+NSAPLMVP DAL G  W+D  AE L Q VRK SNVL+TT+ 
Sbjct: 241 ALKRDGNAIAGLRVAMTGTNSAPLMVPTDALWGRPWNDETAEALVQAVRKVSNVLKTTVA 300

Query: 301 GVKYRRRVLLAISRKVVDQLWEAR 324
           GVKYRRRVLLA++R+ +D LW  +
Sbjct: 301 GVKYRRRVLLAVARRQMDYLWNGK 324


Lambda     K      H
   0.319    0.133    0.399 

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: 422
Number of extensions: 9
Number of successful extensions: 1
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: 324
Length of database: 324
Length adjustment: 28
Effective length of query: 296
Effective length of database: 296
Effective search space:    87616
Effective search space used:    87616
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: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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