GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ltaE in Sinorhizobium meliloti 1021

Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate SMc04029 SMc04029 low specificity L-threonine aldolase

Query= BRENDA::A0T1V9
         (348 letters)



>FitnessBrowser__Smeli:SMc04029
          Length = 348

 Score =  640 bits (1652), Expect = 0.0
 Identities = 318/348 (91%), Positives = 334/348 (95%)

Query: 1   MIFSSDNWAGAHPAIAESLVTHAKGYASAYGTSELDRKVEERFSEVFERDVAVFFVGTGT 60
           MIFSSDNWAGAHPAIAESLV +A+GYASAYGTSELDR+VE+RFSE+FERDVAVFFVGTGT
Sbjct: 1   MIFSSDNWAGAHPAIAESLVANAQGYASAYGTSELDRRVEQRFSEIFERDVAVFFVGTGT 60

Query: 61  AANSLALSIANRAGGIAFCHREAHVNVDECGAPQFFSHGARLSAVGGARGKMDPAKLEAE 120
           AANSLALS ANRAGGIAFCHREAHVNVDECGAP+FFSHGARL  V GARG+M+PAKLEAE
Sbjct: 61  AANSLALSSANRAGGIAFCHREAHVNVDECGAPEFFSHGARLCPVEGARGRMEPAKLEAE 120

Query: 121 IRRFPKENVHGGQPMAVTLTQATESGTVYSLGEIEAIASIARSQTLPLHMDGARFANALV 180
           IRR P+ENVHGGQPMAVTLTQATESGTVYSL +IE I SIARS  LPLHMDGARFANALV
Sbjct: 121 IRRLPRENVHGGQPMAVTLTQATESGTVYSLDQIETIGSIARSHKLPLHMDGARFANALV 180

Query: 181 SLGTTPAEMTWKRGIDLLSFGGTKNGCWCAEALVLFDPSRAQEMHFLRKRSAQLFSKSRF 240
           SLGTTPAEMTWKRG+DLLSFGGTKNGCWCAEALVLFD S+AQEMHFLRKRSAQLFSKSRF
Sbjct: 181 SLGTTPAEMTWKRGVDLLSFGGTKNGCWCAEALVLFDLSKAQEMHFLRKRSAQLFSKSRF 240

Query: 241 VAAQFDAYLAGDLWLDLARHANAMARRLADGITASAESRLAWAPDANEVFVVLKREAASR 300
           VAAQFDAYLAGDLWLDLARHANAMA+RLADGITASA SRLAWAPDANEVFVVLKREAA R
Sbjct: 241 VAAQFDAYLAGDLWLDLARHANAMAQRLADGITASAGSRLAWAPDANEVFVVLKREAAGR 300

Query: 301 LRQQGALFYDWEVPHDLEGSLAEDEGLFRLVTSFATRAEDVDRFVAAC 348
           L++QGALFYDWEVPHDLEGSLAEDEGL+RLVTSFATRAEDVDRFVAAC
Sbjct: 301 LQRQGALFYDWEVPHDLEGSLAEDEGLYRLVTSFATRAEDVDRFVAAC 348


Lambda     K      H
   0.320    0.132    0.394 

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: 497
Number of extensions: 11
Number of successful extensions: 1
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: 348
Length of database: 348
Length adjustment: 29
Effective length of query: 319
Effective length of database: 319
Effective search space:   101761
Effective search space used:   101761
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 (21.9 bits)
S2: 49 (23.5 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