GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Shewanella halifaxensis HAW-EB4

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_012275357.1 SHAL_RS01130 crotonobetainyl-CoA hydratase

Query= BRENDA::Q1D5Y4
         (258 letters)



>NCBI__GCF_000019185.1:WP_012275357.1
          Length = 261

 Score =  148 bits (373), Expect = 1e-40
 Identities = 97/257 (37%), Positives = 135/257 (52%), Gaps = 6/257 (2%)

Query: 6   VDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65
           V   G I   T+D   + NAI      E+GE+        ++R  +ITGAG++ F AG D
Sbjct: 7   VTRNGAILEITLD-RPKANAIDAKTSFEMGEVFLAFREDPELRVAIITGAGERFFSAGWD 65

Query: 66  LKERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPA 125
           LK  A   E     F  G       I   D   IAA+NG A GGG ELALA D+ + +  
Sbjct: 66  LKAAAE-GEAPDADFGPGGFAGLTEIFDLDKPVIAAVNGYAFGGGFELALAADMIICSEN 124

Query: 126 AELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGH 185
           A   L E KLGI+P  GG  RL +L+ P    +L++T R + A EA   G+ NR+     
Sbjct: 125 ASFALPEAKLGIVPDSGGMLRLPKLLPPAIVNELMMTGRGMGAEEALRWGVVNRVVESDK 184

Query: 186 LLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDAL----ALELRKYEEILKTEDRL 241
           L+  A  LA+ + + AP+A+A  K    E + L +++      A  L+ Y  +L++ED L
Sbjct: 185 LMDSARELAQQIAQGAPLAIAAIKEIYRETSELSVEEGYRHIRAGGLKNYPSVLRSEDAL 244

Query: 242 EGLRAFAEKRAPVYKGR 258
           EG  AF+EKR PV+KGR
Sbjct: 245 EGPLAFSEKRDPVWKGR 261


Lambda     K      H
   0.319    0.136    0.380 

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: 143
Number of extensions: 7
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: 258
Length of database: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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