GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pedobacter sp. GW460-11-11-14-LB5

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate CA265_RS15560 CA265_RS15560 glutamate/aspartate:proton symporter GltP

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__Pedo557:CA265_RS15560
          Length = 428

 Score =  509 bits (1310), Expect = e-149
 Identities = 251/411 (61%), Positives = 326/411 (79%), Gaps = 1/411 (0%)

Query: 2   KLFKNLTVQVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAK 61
           K+F NLT QV+ A+IIG+ VG  +P      K +   FIN + M+IAPIIFFTIVLGIA 
Sbjct: 9   KVFSNLTFQVLLAIIIGIYVGAYFPGFAPTAKLISQGFINLISMLIAPIIFFTIVLGIAH 68

Query: 62  MGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGG 121
           MGDMKKVG+VGGKA +YFE+V+T+A+ IGL V N++KPGAG+     +   ++ Y +   
Sbjct: 69  MGDMKKVGRVGGKALLYFEIVSTVAIAIGLLVANVLKPGAGMIAKAGDATKIAGYAEQA- 127

Query: 122 QGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHV 181
           + ++W EF  HI+P N++ +FA+G+ILQ+L F+ILFG GL  LG +G +V++ FDK+S V
Sbjct: 128 KDMNWAEFFLHIIPHNIIASFAEGNILQILLFAILFGYGLNKLGGEGTTVLNAFDKISKV 187

Query: 182 FFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKL 241
            FKI+  IMR APIGAFG MA++IG  GL+SI  +A LM SVY+T FLF+FV LN IC+ 
Sbjct: 188 LFKIMKLIMRLAPIGAFGGMAFSIGTHGLESIVGMAKLMGSVYLTCFLFIFVILNGICRY 247

Query: 242 YGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPTGYSFNLDG 301
           Y FSLW YL++I+ E+LIVLGTSSSES LP MM KME  GC KSVVGLVIPTGYSFNLDG
Sbjct: 248 YNFSLWAYLKYIRQEILIVLGTSSSESALPSMMQKMEAIGCDKSVVGLVIPTGYSFNLDG 307

Query: 302 TSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVI 361
           T+IYL+MA +FL QVF VDL++GQQIT++ VLM+TSKGAAGVTGSGFIVL STL+AL+++
Sbjct: 308 TAIYLAMAVIFLCQVFHVDLTLGQQITVLGVLMITSKGAAGVTGSGFIVLVSTLTALKIM 367

Query: 362 PLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAKSIEAVE 412
           P+E +++L+GVDRFMSE RAI N+IGNG+ATI++AKSE +FDE K ++A++
Sbjct: 368 PIEHISILIGVDRFMSEARAITNVIGNGVATIVIAKSEKQFDEQKYLKAIQ 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: 563
Number of extensions: 21
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: 421
Length of database: 428
Length adjustment: 32
Effective length of query: 389
Effective length of database: 396
Effective search space:   154044
Effective search space used:   154044
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