GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pseudomonas stutzeri RCH2

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate GFF4002 Psest_4075 Na+/H+-dicarboxylate symporters

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__psRCH2:GFF4002
          Length = 419

 Score =  253 bits (645), Expect = 1e-71
 Identities = 140/400 (35%), Positives = 221/400 (55%), Gaps = 14/400 (3%)

Query: 10  QVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAKMGDMKKVG 69
           Q++  + +GV  G+ +    + + P+G  F+NA+KM+I P++F ++V GI  M D  K+G
Sbjct: 22  QILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQDSAKLG 81

Query: 70  KVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGGQGIDWIEF 129
           ++  K    + V T  A+ IGL    +  PG G++        V+   +   Q    +  
Sbjct: 82  RISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNM-------VASGNEQAKQAPSLVSI 134

Query: 130 ITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHVFFKIIGYI 189
           +  +VP+N V AFA+G+ILQ++ F+I  GV +  +GE+G   +  FD ++  F+K+   +
Sbjct: 135 LVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLV 194

Query: 190 MRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKLYGFSLWNY 249
           MR APIG F   A  +G  G + + PLA ++  +Y+     V +    +  L   +  N 
Sbjct: 195 MRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGL--LARLNP 252

Query: 250 LRF---IKDELLIVLGTSSSESVLPRMMD-KMERYGCSKSVVGLVIPTGYSFNLDGTSIY 305
           LRF   I   L +   TSSS   LP  ++   +  G S+ V G V+P G + N+DGT+IY
Sbjct: 253 LRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIY 312

Query: 306 LSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVIPLEG 365
             +  +F+AQ FG+DLS GQ   IIL   L S G AG+ G+G I+L   L+A   +PLEG
Sbjct: 313 QGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAG-LPLEG 371

Query: 366 LALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEA 405
           +AL+ G+DR +   R  VN+ G+ + T +V +SE E D A
Sbjct: 372 VALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRA 411


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: 450
Number of extensions: 19
Number of successful extensions: 4
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: 419
Length adjustment: 32
Effective length of query: 389
Effective length of database: 387
Effective search space:   150543
Effective search space used:   150543
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: 50 (23.9 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