GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kguT in Pseudomonas fluorescens FW300-N2E2

Align KguT (characterized, see rationale)
to candidate Pf6N2E2_628 2-ketogluconate transporter

Query= uniprot:A0A167V864
         (425 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_628 2-ketogluconate
           transporter
          Length = 432

 Score =  699 bits (1803), Expect = 0.0
 Identities = 339/417 (81%), Positives = 365/417 (87%)

Query: 1   MQIDRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFL 60
           MQ   LA RRWWYIMPIVFITYSLAYLDRANYGFAAASGMA DL ITP LSSLLGALFFL
Sbjct: 1   MQTLNLATRRWWYIMPIVFITYSLAYLDRANYGFAAASGMAKDLMITPGLSSLLGALFFL 60

Query: 61  GYFFFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVM 120
           GYFFFQVPGAIYA+K SVKKLIFVSLILWG LATLTG+V +   LI IRF+LGVVEAAVM
Sbjct: 61  GYFFFQVPGAIYAQKHSVKKLIFVSLILWGSLATLTGVVSNAYWLIVIRFMLGVVEAAVM 120

Query: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVL 180
           PAML+YLCHWFTRAERSRANTFLILGNPVT+LWMSVVSGYLV+ FDWRWMFIIEGLPAVL
Sbjct: 121 PAMLVYLCHWFTRAERSRANTFLILGNPVTMLWMSVVSGYLVQQFDWRWMFIIEGLPAVL 180

Query: 181 WAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQY 240
           WAFIWWRL DDRP QA WL  QEK  L  ALAAEQ GIK VKNY EAFRSPKVIIL+LQ+
Sbjct: 181 WAFIWWRLADDRPSQAKWLSDQEKHDLESALAAEQVGIKAVKNYAEAFRSPKVIILALQF 240

Query: 241 FCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300
           FCWSIGVYGFVLWLPSILK    +++V AGWLS++PYL AV+ ML VSWASD+ QKRKRF
Sbjct: 241 FCWSIGVYGFVLWLPSILKAGLQMNMVEAGWLSSLPYLAAVIGMLVVSWASDKAQKRKRF 300

Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360
           VWPPLL+A++AFY SY+LG EHFWWSY+LLV+AGACMYAPYGPFFAIVPE+LP+NVAGGA
Sbjct: 301 VWPPLLVASIAFYASYLLGPEHFWWSYSLLVVAGACMYAPYGPFFAIVPEILPANVAGGA 360

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQAR 417
           MALINSMGALGSF GS+LVGYLNG TG PG S+L M GALLVAV LT  L P    R
Sbjct: 361 MALINSMGALGSFGGSYLVGYLNGSTGSPGMSFLLMSGALLVAVVLTLALKPGASDR 417


Lambda     K      H
   0.328    0.140    0.457 

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: 886
Number of extensions: 37
Number of successful extensions: 1
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: 425
Length of database: 432
Length adjustment: 32
Effective length of query: 393
Effective length of database: 400
Effective search space:   157200
Effective search space used:   157200
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 (21.8 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