GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_04205 in Burkholderia phytofirmans PsJN

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BPHYT_RS24150 BPHYT_RS24150 glucarate transporter

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



>FitnessBrowser__BFirm:BPHYT_RS24150
          Length = 450

 Score =  579 bits (1492), Expect = e-170
 Identities = 272/437 (62%), Positives = 348/437 (79%), Gaps = 6/437 (1%)

Query: 5   KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64
           K T VRY ILL++FL+TT NYADRAT+++ GS+++ + G DA+ +GYIFSAF WAYV  Q
Sbjct: 14  KRTRVRYGILLLIFLITTFNYADRATLSVTGSAMRAEFGFDAIRMGYIFSAFSWAYVLSQ 73

Query: 65  IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFG-VSTAVVALFMLRFMVGLAEAPS 123
           +P GWLLDRFG+++VYA SIF WSLFT+LQ  +G  G  + AV ALF+LRF +G AE+P+
Sbjct: 74  LPAGWLLDRFGARRVYAASIFFWSLFTLLQSSIGLLGSAAAAVTALFVLRFAMGAAESPA 133

Query: 124 FPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGI 183
           FP NA++VA+WFPT ERGTASAIFNSAQYFA V+F PLM W+ ++FGW  V++VMGV+G+
Sbjct: 134 FPANAKVVASWFPTNERGTASAIFNSAQYFAAVVFTPLMAWLTHAFGWHMVYVVMGVMGL 193

Query: 184 IFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQ---DKGKGKKTDGPKWDYIRQL 240
           + +L WLKV+ +P  HP ++ +E  +I   G +++  +     GK + T G  W  +RQL
Sbjct: 194 LLALTWLKVMKNPADHPRVSRSELEYIEQGGGVINGQKKAPSAGKIENTGG--WSLVRQL 251

Query: 241 LTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLG 300
           L+NRM+LGVYL QYCIN +TYFFLTWFP+YLVQ RGMTIL+AG +ASLPAICGF GGVLG
Sbjct: 252 LSNRMLLGVYLAQYCINVLTYFFLTWFPIYLVQARGMTILQAGLVASLPAICGFSGGVLG 311

Query: 301 GVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGAL 360
           G++SD L+R+GHSLT ARK PI+GG+L+S  I+ CNYV  +W+VV  M+LAFFGKG+GAL
Sbjct: 312 GILSDGLIRRGHSLTVARKVPIVGGMLLSVCIIGCNYVSTDWVVVALMSLAFFGKGIGAL 371

Query: 361 GWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVA 420
           GWAVV+DTSP++  GLSG +FN FGN+A I TPIVIGY+++ TGSF  ALVFVG NAL+ 
Sbjct: 372 GWAVVADTSPREALGLSGAIFNMFGNVAGIVTPIVIGYLVAKTGSFNGALVFVGINALLT 431

Query: 421 VFSYLVIVGPIKRVVLK 437
           VFSYLVIV  IKRV L+
Sbjct: 432 VFSYLVIVKDIKRVELR 448


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: 749
Number of extensions: 38
Number of successful extensions: 5
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: 450
Length adjustment: 33
Effective length of query: 421
Effective length of database: 417
Effective search space:   175557
Effective search space used:   175557
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