GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Cupriavidus basilensis 4G11

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate RR42_RS05210 RR42_RS05210 malic enzyme

Query= curated2:Q726S7
         (704 letters)



>FitnessBrowser__Cup4G11:RR42_RS05210
          Length = 773

 Score =  174 bits (442), Expect = 1e-47
 Identities = 112/338 (33%), Positives = 171/338 (50%), Gaps = 10/338 (2%)

Query: 372 RITPKMFEFNLIEK-----AKRNRMRIVLPEGAEERILRAADILVRREVADIILLGDANT 426
           ++T  ++   LI K     AK    R+V  EG EER+LRA   +V   +A  IL+G  + 
Sbjct: 434 QLTQYVYHTGLIMKPVFTAAKAAPKRVVYAEGEEERVLRAVQTVVDEGLARPILIGRPHV 493

Query: 427 VGSRIGDLGLDMDG---VQIVQPNLSPKFDEYVAAYHECRKKKGISMEQARDMMN-DPTY 482
           +  RI   GL +      +++ P   P++  Y  AYH  R + G++ + A+ M+    T 
Sbjct: 494 IQMRIDKAGLRLKAGADFELINPEDDPRYRAYHEAYHTLRGRDGVTPDVAKVMLRRSNTL 553

Query: 483 FGTMMVHKGDADGMVSGAINTTAHTIRPAFEFIKTKPGVSIVSSVFLMCLKDRVLVFGDC 542
            GTM++H GDAD M+ G +      +    + I   PG  + +++  + L+   L   D 
Sbjct: 554 IGTMLMHMGDADAMLCGTVGRFEAHLEHVRDVIGMAPGAKVFAAMNALMLEKYTLFITDT 613

Query: 543 AVNPNPTAEQLAEIAISASHTARIFGVDPRVAMLSYSTGSSGKGADVEKVIEATRIAKER 602
            VN +PTAE+LA I   A+     FG  P+VA++S+S   S       K+  A  I    
Sbjct: 614 FVNDDPTAEELAAITQLAAEEIARFGQHPKVALMSHSMFGSSDRPSARKMRAAQEILARE 673

Query: 603 APELLLEGPLQYDAAIDMDVARTKLPGSTVAGQATVFIFPDLNTGNNTYKAVQRAAG-AV 661
           AP L +EG +Q DAA+  DV R  LPG+ +AG A + + P L+  N  +  ++   G  V
Sbjct: 674 APHLEVEGEMQGDAALVEDVRRHFLPGTKLAGSANLLVMPTLDAANIAFNLLKITGGQGV 733

Query: 662 AIGPVLQGLNKPVNDLSRGCTVADIVNTVAITAIQAQA 699
            IGP+L G  KPV+ L+   T   IVN  A+   +A A
Sbjct: 734 TIGPILLGAAKPVHILNPQATTRRIVNMTAVAVAEANA 771


Lambda     K      H
   0.319    0.135    0.383 

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: 1179
Number of extensions: 64
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: 704
Length of database: 773
Length adjustment: 40
Effective length of query: 664
Effective length of database: 733
Effective search space:   486712
Effective search space used:   486712
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 (21.7 bits)
S2: 55 (25.8 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