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_RS30935 BPHYT_RS30935 MFS transporter

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



>FitnessBrowser__BFirm:BPHYT_RS30935
          Length = 439

 Score =  221 bits (564), Expect = 3e-62
 Identities = 134/438 (30%), Positives = 215/438 (49%), Gaps = 28/438 (6%)

Query: 14  LLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGWLLDR 73
           L +L +   +NY DR T+A+A   ++ DLG+    +G + SAF W+Y   Q+P G L+DR
Sbjct: 22  LTLLMVSGIVNYLDRGTLAVANPLIRHDLGLSLGEMGLLLSAFSWSYALFQLPVGGLVDR 81

Query: 74  FGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFPGNARIVAA 133
            G +K+  + +  WSL     G+V  FG         + R ++G+ EAP FP  AR+V+ 
Sbjct: 82  IGPRKLLGIGLIVWSLAQASGGFVSTFGW------FILARIVLGIGEAPQFPSAARVVSN 135

Query: 134 WFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSLIWLKVI 193
           WFP   RG  + IFNSA    T L    +  +V  F W+  FIV GV+G++ +L+WL V 
Sbjct: 136 WFPLRARGKPTGIFNSASPLGTALAPLCLSVLVVQFHWRWAFIVTGVVGLVVALVWLAVY 195

Query: 194 HSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRMMLGVYLGQ 253
             P +  M  EAE +++  +      D D+         +W   R L ++    G+ +G 
Sbjct: 196 RDPVKATM-TEAERHYLEGD------DADRKPAPTVTFAEW---RSLFSHGTTWGMLIGF 245

Query: 254 YCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISDYLLRKGHS 313
           +    + + +LTW P YL  +R M+++  G  AS+P  CGF+G +  G  SD +  +  S
Sbjct: 246 FGSVYLNWVYLTWLPGYLTMERHMSLMHTGVAASIPFFCGFLGSLTAGWFSDLITSRSTS 305

Query: 314 LTFARKAPIIGGLL------ISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVVSD 367
              +R+  ++  +L      I +++V  N +     +V    + F      A  WA+ + 
Sbjct: 306 PVASRRNAVVIAMLGMVAFTIPAALVESNTI----AIVCISVVIFLANAASASSWALATA 361

Query: 368 TSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYLVI 427
            +P    G  G + N  G L     PI+ GY I+ + SF  AL+     A +   SYL++
Sbjct: 362 AAPPNRVGSLGAIQNFGGFLGGALAPILTGY-IAQSWSFVPALLTAAGIAFIGAMSYLLL 420

Query: 428 V-GPIKRVVLKEPPTQGP 444
           V  PI+       P + P
Sbjct: 421 VRKPIEDPSTPTEPVRAP 438


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: 659
Number of extensions: 40
Number of successful extensions: 7
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: 439
Length adjustment: 33
Effective length of query: 421
Effective length of database: 406
Effective search space:   170926
Effective search space used:   170926
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