GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Marinobacter algicola DG893

Align (4E)-oxalomesaconate Delta-isomerase; OMA isomerase; 1,3-allylic isomerase LigU; EC 5.3.3.- (characterized)
to candidate WP_007153590.1 MDG893_RS09680 2-methylaconitate cis-trans isomerase PrpF

Query= SwissProt::Q0KJL4
         (357 letters)



>NCBI__GCF_000170835.1:WP_007153590.1
          Length = 390

 Score =  188 bits (478), Expect = 2e-52
 Identities = 143/381 (37%), Positives = 195/381 (51%), Gaps = 38/381 (9%)

Query: 12  PCMWMRGGTSKGGYFLRADLPADTAA----RDAFLLAVMGSPDP--RQIDGMGGADPLTS 65
           P  +MRGGTSKG +F   DLP         RD+ L+ V+GSPDP  +QIDG+G     TS
Sbjct: 10  PATYMRGGTSKGVFFRLEDLPEGAQTPGPIRDSLLMRVIGSPDPYQKQIDGLGNGTSSTS 69

Query: 66  KVAVVSKSERPGIDVDYLFLQVFVDQAIVTDAQNCGNILAGVGPFAIERGLVAASGDE-- 123
           K  +VS+SERP  DVDYLF QV +D+A V  + NCGN+   VG FAI  GLVAA   E  
Sbjct: 70  KTVIVSRSERPDHDVDYLFGQVGIDRAFVDWSGNCGNLTTAVGAFAISAGLVAADTLEQN 129

Query: 124 --TRVAIFMENTGQVAVATVRTPGGSVTYAGDAAIDGVPGTHAPIPTEFRDTAGSSCGAL 181
               V I+  N G+  +A V    G V   GD  +DGV    A I  EF D AG   GA+
Sbjct: 130 SVAAVRIWQANIGKTIIARVPMTDGQVQETGDFELDGVAFPAAKIALEFLDPAGDE-GAI 188

Query: 182 LPSGNAVDV--VNGL---PVTLIDNGMPCVVMKAADVGITGYEDRDSLDANAELKAKIEA 236
            P+GN VD   V GL    VT+I  G+P + ++A  VG TG E +D+++ + +  A  E+
Sbjct: 189 FPTGNPVDELDVPGLGKFRVTMITAGIPTIFVEADAVGYTGTELQDAINNDPQALAMFES 248

Query: 237 IR----LAVGELMNLGDVTEKS-VPKMMLVAPPRDGGA------------VCVRSFIPHR 279
           IR    L +G +  L +   +   PK+  VA P D  A            + VR     +
Sbjct: 249 IRGHGALQMGLVETLAEAENRQHTPKIAFVAGPSDYVAASGKRITIDDVDLLVRGLSMGK 308

Query: 280 AHATIGVLGAVSVATACLIPGSPAAEVAVVPEGARKTLSIEHPTGEMSCVLEVDDAGN-- 337
            H  +    AV++  A  IPG+     A    G + ++   HP+G +    E  ++    
Sbjct: 309 LHHAMPGTVAVAIGAAHAIPGTIVNTAA--GGGNQTSVRFGHPSGTLRVGAEARESNGEW 366

Query: 338 -VVSAALLRTARKLMDGVVFV 357
            V  A + R+AR LM+G V V
Sbjct: 367 VVEKAIMSRSARVLMEGWVRV 387


Lambda     K      H
   0.318    0.135    0.396 

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: 393
Number of extensions: 21
Number of successful extensions: 6
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: 357
Length of database: 390
Length adjustment: 30
Effective length of query: 327
Effective length of database: 360
Effective search space:   117720
Effective search space used:   117720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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