GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Hafnia paralvei ATCC 29927

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_008814119.1 M988_RS06145 NADP-dependent oxaloacetate-decarboxylating malate dehydrogenase

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



>NCBI__GCF_001655005.1:WP_008814119.1
          Length = 759

 Score =  177 bits (448), Expect = 1e-48
 Identities = 102/332 (30%), Positives = 187/332 (56%), Gaps = 12/332 (3%)

Query: 4   IESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNLDI 63
           ++ I+  AK++KKR++LAEGEE+R L A  +++  G+A  +LVG  + I+ +  +L L I
Sbjct: 431 MKPIFSQAKKEKKRVVLAEGEEERVLHATQELVTLGIASPILVGRPDVIEMRLKKLGLQI 490

Query: 64  SKA---EIMDPETSLKTETYARDFYELRKHKGMTIEKSEK-MVRDPLYFATMALKDGYVD 119
                 EI++ E+  +   Y R++Y++ K +G++ E++ + ++ +P   A + L+ G  D
Sbjct: 491 EAGKDFEIVNNESDPRFNEYWREYYDIMKRRGVSQEQARRAVIGNPTLIAAIMLQRGEAD 550

Query: 120 GMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNP 179
            M+ G +    +       +     G  +      +++P       G    AD  VN +P
Sbjct: 551 AMICGTIGNYHEHYEVVHNVFGFREGAHVAGAMNALLLPS------GNTFIADTYVNDDP 604

Query: 180 TSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLA 239
           T+++LA+I +  AET R+   +EPKVA+LS S+ G++      K++  +E+  +  P+L 
Sbjct: 605 TAEQLAEITLMAAETVRRF-GIEPKVALLSHSSFGASDCPAARKMRRTLELVNEAAPELE 663

Query: 240 IDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQ-RFAKAKAIGPI 298
           IDGE+  DAA+   +     P S + G AN+L+ P+++   I Y L++   ++   +GP+
Sbjct: 664 IDGEMHGDAALVESIRNDVMPDSPLKGAANILIMPNMEAARISYNLLRVSSSEGVTVGPV 723

Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330
             G +KP++ L+   S   IVN+VA++VV+AQ
Sbjct: 724 LMGVSKPVHILTSIASVRRIVNMVALSVVEAQ 755


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: 540
Number of extensions: 23
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: 759
Length adjustment: 34
Effective length of query: 299
Effective length of database: 725
Effective search space:   216775
Effective search space used:   216775
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 24 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