GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Cupriavidus basilensis 4G11

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate RR42_RS12250 RR42_RS12250 sulfate ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__Cup4G11:RR42_RS12250
          Length = 374

 Score =  117 bits (293), Expect = 3e-31
 Identities = 81/228 (35%), Positives = 120/228 (52%), Gaps = 7/228 (3%)

Query: 1   MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60
           M+++ +N+   +G    L+DV+L    G++TAL+GP+GCGK+TLL   + L    +G + 
Sbjct: 1   MSIQVKNVQKHFGNFVALDDVTLDFDEGQLTALLGPSGCGKTTLLRIIAGLERADAGQIL 60

Query: 61  LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGR--NPWLSLWGRLSAEDNAR 118
           L     +    RQ  R++  + QH+   + +TV E V++G    P     G     D  +
Sbjct: 61  LEGRDASHQHVRQ--RQVGFVFQHYALFKHMTVFENVAFGLRVKPRAERPGEAQIRD--K 116

Query: 119 VNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLM 178
           V   +   +++ LA R   +LSGGQRQR  LA  LA    V+LLDEP   LD   + +L 
Sbjct: 117 VRALLELVQLDWLADRYPPQLSGGQRQRIALARALAVEPRVLLLDEPFGALDAKVRKELR 176

Query: 179 RLMGELRTQ-GKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225
           R +  L  +   T V V HD  +A    DQ+V+M  GHV   GTPE V
Sbjct: 177 RWLRRLHDELHVTSVFVTHDQEEALEVADQVVLMNRGHVEQAGTPEAV 224


Lambda     K      H
   0.320    0.134    0.393 

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: 201
Number of extensions: 10
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: 255
Length of database: 374
Length adjustment: 27
Effective length of query: 228
Effective length of database: 347
Effective search space:    79116
Effective search space used:    79116
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:

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