GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:17200
          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:

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