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_RS02510 BPHYT_RS02510 C4-dicarboxylate ABC transporter

Query= TCDB::Q01857
         (444 letters)



>FitnessBrowser__BFirm:BPHYT_RS02510
          Length = 426

 Score =  547 bits (1410), Expect = e-160
 Identities = 272/415 (65%), Positives = 335/415 (80%)

Query: 15  KKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGI 74
           KKP +  LYVQV+VAI  GI LGHFYP L   +KPLGD FIKL+KM+I P+IF TV TGI
Sbjct: 2   KKPIHKVLYVQVIVAIIIGIALGHFYPNLAVDMKPLGDGFIKLIKMVIGPIIFCTVVTGI 61

Query: 75  AGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFA 134
           AGM D++KVGRV GKA+LYF   ST AL++GLI  +V++PG G NIDPA+LD  AVA++A
Sbjct: 62  AGMEDMKKVGRVGGKALLYFEIVSTFALVLGLIATHVLKPGVGFNIDPATLDGKAVASYA 121

Query: 135 AKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSL 194
           AKAH Q+ V FL ++IP T+V AFA G+ILQ+L  ++LFG  LA  GEKG+ V +F++ L
Sbjct: 122 AKAHGQTTVDFLMHLIPDTLVSAFAQGEILQILLIALLFGAVLATAGEKGKVVTSFIDGL 181

Query: 195 TAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGAV 254
           +  +F +V I+ K APIGAFGAMAFTIGKYG+GS+  +  LIGTFY+TS++FV +VLG +
Sbjct: 182 SHVLFGIVRIITKLAPIGAFGAMAFTIGKYGIGSLLPMLKLIGTFYLTSIVFVVVVLGII 241

Query: 255 ARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFN 314
           AR  GF+I+  + YIKEE+L+VLGTSSSEAALP LM K+EK GC RSVVGLV+PTGYSFN
Sbjct: 242 ARAVGFNILRFVAYIKEEMLIVLGTSSSEAALPQLMLKLEKLGCSRSVVGLVVPTGYSFN 301

Query: 315 LDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVV 374
           LDGTNIYMT+A LFIAQAT   L+W  Q+ LL V ML+SKGA+G+TGAGFITLAATL+VV
Sbjct: 302 LDGTNIYMTMAVLFIAQATNTDLTWTQQLTLLAVTMLTSKGASGVTGAGFITLAATLAVV 361

Query: 375 PSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAALGG 429
           P++P++GM LILGIDRFMSECRALTN+VGN VAT+VV+ WE ELD  +L AAL G
Sbjct: 362 PTIPLSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNKLNAALRG 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: 635
Number of extensions: 32
Number of successful extensions: 2
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: 426
Length adjustment: 32
Effective length of query: 412
Effective length of database: 394
Effective search space:   162328
Effective search space used:   162328
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