GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pseudomonas fluorescens FW300-N2E3

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate AO353_10990 AO353_10990 glutamate:protein symporter

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10990
          Length = 443

 Score =  365 bits (936), Expect = e-105
 Identities = 178/413 (43%), Positives = 281/413 (68%), Gaps = 13/413 (3%)

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

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

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

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

Query: 234 ALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPT 293
            L +I +L+GFS+   +R  KDEL++   T+SSE+VLPR+++KME YG  K++   V+PT
Sbjct: 247 VLGLIARLFGFSVIKLMRIFKDELVLAYSTASSETVLPRVIEKMEAYGAPKAICSFVVPT 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 ++V++ E  +D+AK
Sbjct: 367 TLGSVG-IPLEGLAFIAGVDRIMDMARTALNVIGNALAVLVVSRWEGMYDDAK 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: 495
Number of extensions: 17
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:

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