GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Xanthobacter autotrophicus Py2

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_198139304.1 XAUT_RS15790 NADP-dependent malic enzyme

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



>NCBI__GCF_000017645.1:WP_198139304.1
          Length = 756

 Score =  174 bits (440), Expect = 8e-48
 Identities = 101/332 (30%), Positives = 178/332 (53%), Gaps = 11/332 (3%)

Query: 3   LIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNLD 62
           ++  ++  AK++ KR++ AEGE++R L A   +++EG+A  ++V   N ++ +     L 
Sbjct: 429 IMRPLFAQAKRNIKRVVYAEGEDERVLRAVQAVVEEGIARPIIVARPNVLETRLKRFGLS 488

Query: 63  ISKA---EIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRD-PLYFATMALKDGYV 118
           +      ++++PE   +   Y RD+ E+   +G+T + +  +VR  P   A +A+K G  
Sbjct: 489 VRPGHDFDLINPEDDPRYRDYVRDYVEIAGRRGVTPDAARTLVRTHPTVIAALAVKRGEA 548

Query: 119 DGMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPN 178
           D M+ G        LR    II  APGVK ++   ++I         G     D  +   
Sbjct: 549 DAMLCGIEGRFTRHLRQVRDIIGLAPGVKELAALSLLIT------SHGNFFICDTQIQTE 602

Query: 179 PTSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDL 238
           PT+ +LA++ +  A   R+   +EP+VA+LS S  GS +     +V++A+ I ++  P+L
Sbjct: 603 PTAADLAEMTVLAAAHVRRF-GLEPRVALLSHSNFGSHETLSAKRVRSALSIIREREPNL 661

Query: 239 AIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPI 298
            +DGE+Q D+A+  ++     P+S + G ANVLV PDL   +I + +++    A  +GPI
Sbjct: 662 EVDGEMQADSALLEDIRKRVLPNSTLTGAANVLVMPDLDAADIAFNMLKVLGDALPVGPI 721

Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330
             G AKP + L    ++  IVN+ A+ V +AQ
Sbjct: 722 LMGTAKPAHILGPSVTARGIVNMTAVAVAEAQ 753


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: 550
Number of extensions: 26
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: 333
Length of database: 756
Length adjustment: 34
Effective length of query: 299
Effective length of database: 722
Effective search space:   215878
Effective search space used:   215878
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 Apr 09 2024. 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