GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Klebsiella michiganensis M5al

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate BWI76_RS05690 BWI76_RS05690 fumarylacetoacetate (FAA) hydrolase

Query= reanno::Smeli:SM_b21112
         (281 letters)



>FitnessBrowser__Koxy:BWI76_RS05690
          Length = 282

 Score =  166 bits (421), Expect = 4e-46
 Identities = 108/292 (36%), Positives = 158/292 (54%), Gaps = 25/292 (8%)

Query: 1   MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDP---SKLDELANLDV-ETLPA 56
           MKLL +    + K GL  +DG+I DL          AL P   S L+ L +L + +TLP 
Sbjct: 1   MKLLSFRVNDKNKYGLATADGVI-DLQ---------ALFPQYGSLLEFLPHLHLLDTLPP 50

Query: 57  VSGNPRLG-------PCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPN 109
            +             P +    K IC G+NY D     G   P  P++F++   +  G  
Sbjct: 51  SAKKTHYSFNEIAFLPVITEPKKIICAGVNYRDKNV-VGNEKPANPVLFIRFADSQTGHL 109

Query: 110 DDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQW 169
             L+ P  S + D+E E+ +VIG+  + + E EAL YVAGY    D S R +Q   H  +
Sbjct: 110 APLLKPERSNEFDYEGEMALVIGRGGRNIPEQEALQYVAGYSCYMDGSVRDWQ---HTCF 166

Query: 170 TKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQ 229
           T GK+    G  GPWLVT D++ DPQ+L +  ++NG+T+Q  +T +M+Y  A L++Y+S 
Sbjct: 167 TGGKNWPATGGFGPWLVTADDIPDPQNLNITTRLNGQTVQQDNTGSMLYSIAELIAYIST 226

Query: 230 FMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRADA 281
           F +L PGD+I TGTP G+G    PP +++ GD VE+ IE +G     V +DA
Sbjct: 227 FSALSPGDVILTGTPGGIGKKRTPPLFMQPGDKVEVEIEQIGCLIHTVCSDA 278


Lambda     K      H
   0.315    0.136    0.408 

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: 244
Number of extensions: 16
Number of successful extensions: 4
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: 281
Length of database: 282
Length adjustment: 26
Effective length of query: 255
Effective length of database: 256
Effective search space:    65280
Effective search space used:    65280
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: 42 (22.0 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