GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_04205 in Escherichia coli BW25113

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate 17200 b3127 predicted (D)-galactarate transporter (NCBI)

Query= reanno::WCS417:GFF828
         (454 letters)



>lcl|FitnessBrowser__Keio:17200 b3127 predicted (D)-galactarate
           transporter (NCBI)
          Length = 444

 Score =  582 bits (1500), Expect = e-171
 Identities = 270/434 (62%), Positives = 349/434 (80%)

Query: 5   KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64
           K  H RYLILL++F+VT +NYADRAT++IAG+ + K+L + AV++GYIFSAFGWAY+  Q
Sbjct: 11  KGVHTRYLILLIIFIVTAVNYADRATLSIAGTEVAKELQLSAVSMGYIFSAFGWAYLLMQ 70

Query: 65  IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSF 124
           IPGGWLLD+FGSKKVY  S+F WSLFT LQG+V  F ++ A +++F +RFM+G +EAPSF
Sbjct: 71  IPGGWLLDKFGSKKVYTYSLFFWSLFTFLQGFVDMFPLAWAGISMFFMRFMLGFSEAPSF 130

Query: 125 PGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGII 184
           P NARIVAAWFPT ERGTASAIFNSAQYF+  LF+PL+GW+ +++GW+HVF VMGVIG +
Sbjct: 131 PANARIVAAWFPTKERGTASAIFNSAQYFSLALFSPLLGWLTFAWGWEHVFTVMGVIGFV 190

Query: 185 FSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNR 244
            + +W+K+IH+P  HP ++  E   I+ NGA+VDMD  K       GPK  YI+QLL+NR
Sbjct: 191 LTALWIKLIHNPTDHPRMSAEELKFISENGAVVDMDHKKPGSAAASGPKLHYIKQLLSNR 250

Query: 245 MMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVIS 304
           MMLGV+ GQY IN IT+FFLTWFP+YLVQ++GM+ILK G +AS+PA+CGF GGVLGGV S
Sbjct: 251 MMLGVFFGQYFINTITWFFLTWFPIYLVQEKGMSILKVGLVASIPALCGFAGGVLGGVFS 310

Query: 305 DYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAV 364
           DYL+++G SLT ARK PI+ G+L++S+I+ CNY +   +VV  MALAFFGKG GALGW V
Sbjct: 311 DYLIKRGLSLTLARKLPIVLGMLLASTIILCNYTNNTTLVVMLMALAFFGKGFGALGWPV 370

Query: 365 VSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSY 424
           +SDT+PK+I GL GG+FN FGN+ASI TP+VIGY++S   SF  ALVFVG +AL+A+  Y
Sbjct: 371 ISDTAPKEIVGLCGGVFNVFGNVASIVTPLVIGYLVSELHSFNAALVFVGCSALMAMVCY 430

Query: 425 LVIVGPIKRVVLKE 438
           L +VG IKR+ L++
Sbjct: 431 LFVVGDIKRMELQK 444


Lambda     K      H
   0.327    0.142    0.444 

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: 787
Number of extensions: 34
Number of successful extensions: 3
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: 454
Length of database: 444
Length adjustment: 33
Effective length of query: 421
Effective length of database: 411
Effective search space:   173031
Effective search space used:   173031
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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