GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Burkholderia phytofirmans PsJN

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate BPHYT_RS13510 BPHYT_RS13510 C4-dicarboxylate transporter

Query= TCDB::Q01857
         (444 letters)



>FitnessBrowser__BFirm:BPHYT_RS13510
          Length = 416

 Score =  501 bits (1290), Expect = e-146
 Identities = 254/414 (61%), Positives = 319/414 (77%), Gaps = 1/414 (0%)

Query: 15  KKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGI 74
           +KP Y  LYVQV+VAI  G+ LGHF P     +KPLGDAFIKLV+MII+PVIF TV TGI
Sbjct: 3   RKPLYKVLYVQVIVAIIIGVALGHFLPADAVAMKPLGDAFIKLVRMIISPVIFCTVVTGI 62

Query: 75  AGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFA 134
           A M D++KVGRV GKA+LYF   STLAL IGL+ A+V++PG G N+DP++LD  A+A++A
Sbjct: 63  ASMHDMRKVGRVGGKALLYFEVVSTLALAIGLLAAHVLKPGIGFNVDPSTLDAGAIASYA 122

Query: 135 AKA-HEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNS 193
           A+A H + + GF  +IIP T  GAF  GDIL VL  ++LFG ALA++GE  + ++  ++ 
Sbjct: 123 AQAAHGEGLAGFFMHIIPDTFAGAFTQGDILPVLLIAMLFGTALAVLGEPAKPLIGLIDL 182

Query: 194 LTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGA 253
           L+   F++V ++   APIGAFGA+AFTIGKYG+ S+  +  LIGTFY+T+ LFV   LG 
Sbjct: 183 LSKTFFRIVRMITSLAPIGAFGAIAFTIGKYGIVSLLPMMKLIGTFYLTAFLFVSCGLGL 242

Query: 254 VARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSF 313
           +AR  GFS+   + YIK+ELL+VLGTS+SEAALP LM K+E+ GC R +VGLV+PTGYSF
Sbjct: 243 IARACGFSLWRFVVYIKDELLIVLGTSTSEAALPQLMEKLERLGCSRGIVGLVVPTGYSF 302

Query: 314 NLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSV 373
           NLDGTNIYMTLA LF+AQAT  HL+   +I LL V ML+SKG+ G+TGAGFITLAA+LSV
Sbjct: 303 NLDGTNIYMTLAVLFLAQATNTHLTIAQEITLLAVTMLTSKGSTGVTGAGFITLAASLSV 362

Query: 374 VPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAAL 427
           VP+VPV  M LILGIDRFMSECRALTN +GN VA+IV+A WE ELD  +L AAL
Sbjct: 363 VPTVPVTAMVLILGIDRFMSECRALTNTMGNGVASIVIAAWEKELDRGKLNAAL 416


Lambda     K      H
   0.324    0.139    0.393 

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: 588
Number of extensions: 37
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: 444
Length of database: 416
Length adjustment: 32
Effective length of query: 412
Effective length of database: 384
Effective search space:   158208
Effective search space used:   158208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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