GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_011383077.1 AMB_RS03265 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>NCBI__GCF_000009985.1:WP_011383077.1
          Length = 258

 Score =  291 bits (744), Expect = 1e-83
 Identities = 146/258 (56%), Positives = 189/258 (73%)

Query: 1   MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60
           M+   I  ET+G VG+I LNRP  +NAL  AL+  LG AL AF+ADD IGA+V+ G+ +A
Sbjct: 1   MAFENITVETRGNVGVIALNRPKAMNALCAALISELGQALDAFEADDSIGAVVLTGSEKA 60

Query: 61  FAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120
           FAAGADI  MA+ SY DVY +NFIT  WE + + RKP++AAVAG A GGGCE+A+ CD +
Sbjct: 61  FAAGADIKEMASKSYMDVYLANFITDGWERVTKCRKPIVAAVAGFALGGGCEMAMMCDFI 120

Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180
           IAG +AKF  PEI +G +PGAGGTQRL RA+GK+KAM+MCL+ R ++A EA+R GLVSR+
Sbjct: 121 IAGDNAKFGQPEITIGTIPGAGGTQRLTRAVGKSKAMEMCLTGRMMDAAEAERAGLVSRI 180

Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240
           V    L DE V  A  IA+ S P +M  KES+N AFE+TLA+G+ FERR  H+ F++ D 
Sbjct: 181 VPVAELLDEAVKAAGKIASLSRPIVMLCKESVNAAFETTLAQGVTFERRLFHSTFSTEDQ 240

Query: 241 REGIQAFLEKRAPCFSHR 258
           +EG+ AF+EKR   F +R
Sbjct: 241 KEGMAAFVEKRPAAFKNR 258


Lambda     K      H
   0.321    0.135    0.389 

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: 162
Number of extensions: 2
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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 (21.9 bits)
S2: 47 (22.7 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