GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sinorhizobium meliloti 1021

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate SMc01126 SMc01126 malic enzyme

Query= metacyc::PTACLOS-MONOMER
         (333 letters)



>FitnessBrowser__Smeli:SMc01126
          Length = 761

 Score =  150 bits (379), Expect = 1e-40
 Identities = 101/329 (30%), Positives = 163/329 (49%), Gaps = 12/329 (3%)

Query: 4   IESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNLDI 63
           ++ I E  ++  KRI+ AEGEE + + +A     + L   +L+G E  ++E A    +D+
Sbjct: 440 LQRIVERVRRQPKRIVFAEGEEVQMMRSAIAYANQQLGTALLLGREEVMRETAEREGIDL 499

Query: 64  SKA--EIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVR-DPLYFATMALKDGYVDG 120
            +A  +I++   S +   Y    Y   + KG      ++++  D  +FA   +  G  DG
Sbjct: 500 DRAGIQIVNARLSKRVGAYTDFLYSRLQRKGYLFRDVQRLINTDRNHFAASMVALGDADG 559

Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180
           MV+G        L    + I   PG +++     +            +L AD AV+  PT
Sbjct: 560 MVTGLTRNYSTALEDVRRCIDPKPGHRVIGVSIALC-------RGRTVLVADTAVHDMPT 612

Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240
           S+ELADIA   A  A++L  V P+VAML++ST G   GE  ++V+ AV+I  + R D   
Sbjct: 613 SEELADIAEEAAGLAKRLGYV-PRVAMLAYSTFGHPSGERSERVREAVKILDRRRVDFEY 671

Query: 241 DGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQ 300
           DGE+  D A+++ V   + P   ++G ANVLV P   + +I  K++Q    +  IGP+  
Sbjct: 672 DGEMAADVALNARVME-QYPFCRLSGTANVLVMPAFHSASISTKMLQELGGSTVIGPLLV 730

Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQA 329
           G  K +   S      D+VN+ AI    A
Sbjct: 731 GLDKSVQIASMSAKDSDLVNLAAIAAYNA 759


Lambda     K      H
   0.316    0.134    0.374 

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: 504
Number of extensions: 26
Number of successful extensions: 5
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: 333
Length of database: 761
Length adjustment: 34
Effective length of query: 299
Effective length of database: 727
Effective search space:   217373
Effective search space used:   217373
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 (21.6 bits)
S2: 52 (24.6 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