GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctA in Pseudomonas fluorescens GW456-L13

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate PfGW456L13_578 Glutamate-aspartate carrier protein

Query= TCDB::P96603
         (421 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_578
           Glutamate-aspartate carrier protein
          Length = 443

 Score =  364 bits (935), Expect = e-105
 Identities = 177/413 (42%), Positives = 280/413 (67%), Gaps = 13/413 (3%)

Query: 6   NLTVQVITAVIIGVIVGLVWPDVGKE--------MKPLGDTFINAVKMVIAPIIFFTIVL 57
           +L  Q++  +++G+ +G +      E        ++P GD FI  +KM++ PI+  ++++
Sbjct: 7   SLAWQILIGLVLGIAIGALLNHFSAEKAWWISNVLQPAGDIFIRLIKMIVIPIVISSLIV 66

Query: 58  GIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYT 117
           GIA +GD KK+G++G K  IYFE+VTT+A+++GL + N+  PGAG+D S L   D+S+Y 
Sbjct: 67  GIAGVGDAKKLGRIGFKTIIYFEIVTTIAIVVGLLLANLFHPGAGIDMSTLGTVDISKYQ 126

Query: 118 QNGGQGID---WIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAAL-GEKGKSVID 173
               +      +IE I +++PSN+  A  +G++L ++FFS+LFG+GL++L  +  + ++ 
Sbjct: 127 ATAAEVQHEHAFIETILNLIPSNIFAAMVRGEMLPIIFFSVLFGLGLSSLQADLREPLVK 186

Query: 174 FFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFV 233
            F  VS   FK+   IM  APIG F  +A T+ +FG  S+ PLA L++ VY+ +  F FV
Sbjct: 187 MFQGVSESMFKVTHMIMNYAPIGVFALIAVTVANFGFASLIPLAKLVILVYVAIAFFAFV 246

Query: 234 ALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPT 293
            L +I +L+GFS+   +R  KDEL++   T+SSE+VLPR+++KME YG  K++   V+PT
Sbjct: 247 ILGLIARLFGFSVIKLMRIFKDELVLAYSTASSETVLPRVIEKMEAYGAPKAICSFVVPT 306

Query: 294 GYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLAS 353
           GYSFNLDG+++Y S+A +F+AQ++G+DLSI QQ+ ++L LM+TSKG AGV G  F+VL +
Sbjct: 307 GYSFNLDGSTLYQSIAAIFIAQLYGIDLSISQQLLLVLTLMVTSKGIAGVPGVSFVVLLA 366

Query: 354 TLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAK 406
           TL ++  IPLEGLA + GVDR M   R  +N+IGN +A +++A+ E  +D+AK
Sbjct: 367 TLGSVG-IPLEGLAFIAGVDRVMDMARTALNVIGNALAVLVIARWEGMYDDAK 418


Lambda     K      H
   0.326    0.143    0.408 

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: 493
Number of extensions: 15
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: 421
Length of database: 443
Length adjustment: 32
Effective length of query: 389
Effective length of database: 411
Effective search space:   159879
Effective search space used:   159879
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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