GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Marinobacter adhaerens HP15

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF929 HP15_908 enoyl-CoA hydratase/isomerase

Query= BRENDA::Q1D5Y4
         (258 letters)



>FitnessBrowser__Marino:GFF929
          Length = 259

 Score =  155 bits (391), Expect = 1e-42
 Identities = 98/258 (37%), Positives = 142/258 (55%), Gaps = 8/258 (3%)

Query: 5   KVDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGA 64
           +++ RG I + TI+     N  ++  L  L  +V  ++  RD+ A+V+TG G+K + AGA
Sbjct: 6   QLEKRGHIAVLTINNPPA-NTWTKDSLIALTNIVKELNEDRDIFALVMTGQGEKFYSAGA 64

Query: 65  DLKERATMAE-DEVRAFLDG--LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRV 121
           DLK   T A+ D+ RA   G      F  +++   V IAA+NG A+GGG E A+ACD+R+
Sbjct: 65  DLK---TFADGDKARANEMGQLFGEAFSTLQRFRGVSIAAVNGYAMGGGLECAMACDIRI 121

Query: 122 AAPAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLA 181
           A   A++ L E  +G++P  GGTQ L  LVG G AK +IL   R+ A  A  +GL   + 
Sbjct: 122 AEEHAQMALPEAGVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVKADTALRIGLVEEVV 181

Query: 182 PEGHLLAVAYGLAESVVENAPIAVATAKHAI-DEGTGLELDDALALELRKYEEILKTEDR 240
           P G  L  A  LAE   + +P + A  K  +     G   DD   +E   + E+  TED+
Sbjct: 182 PSGQGLDKALELAEMACQQSPSSTARCKTLVMSARDGRSHDDGWRMERELFVELFSTEDQ 241

Query: 241 LEGLRAFAEKRAPVYKGR 258
            EG+ AF EKR P +K R
Sbjct: 242 KEGVNAFLEKRKPEWKNR 259


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: 6
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: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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