GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Pseudomonas simiae WCS417

Align KguT (characterized, see rationale)
to candidate GFF2463 PS417_12560 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__WCS417:GFF2463
          Length = 430

 Score =  706 bits (1821), Expect = 0.0
 Identities = 338/417 (81%), Positives = 369/417 (88%)

Query: 1   MQIDRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFL 60
           M+  +LA RRWWYIMPIVFITYSLAYLDRANYGFAAASGMA+DL ITP +SSLLGALFFL
Sbjct: 1   METVKLATRRWWYIMPIVFITYSLAYLDRANYGFAAASGMAEDLMITPGMSSLLGALFFL 60

Query: 61  GYFFFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVM 120
           GYFFFQVPGAIYA+KRSVKKLIFVSLILWGGLATLTG+V +  +LI IRF+LGVVEAAVM
Sbjct: 61  GYFFFQVPGAIYAQKRSVKKLIFVSLILWGGLATLTGVVSNAYMLIVIRFMLGVVEAAVM 120

Query: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVL 180
           PAML+YLCHWFTRAERSRANTFLILGNPVT+LWMSVVSGYLV+HF WRWMFIIEGLPAVL
Sbjct: 121 PAMLVYLCHWFTRAERSRANTFLILGNPVTMLWMSVVSGYLVQHFSWRWMFIIEGLPAVL 180

Query: 181 WAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQY 240
           WAFIWW+L D+RP+ A WL   EK  L  ALAAEQ GIK VKNY EAFRSPKVIIL+LQ+
Sbjct: 181 WAFIWWKLADERPKDAKWLSDSEKQDLETALAAEQVGIKAVKNYAEAFRSPKVIILALQF 240

Query: 241 FCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300
           FCWSIGVYGFVLWLPSILKQ   +D+V AGWLSA+PYL AV+ ML VSW SD++QKRKRF
Sbjct: 241 FCWSIGVYGFVLWLPSILKQGLQMDMVEAGWLSALPYLAAVIGMLAVSWGSDKLQKRKRF 300

Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360
           VWPPLLIA++AFY SY+LG EHFWWSYTLLVIAGACMYAPYGPFFAIVPE+LP+NVAGGA
Sbjct: 301 VWPPLLIASIAFYASYVLGAEHFWWSYTLLVIAGACMYAPYGPFFAIVPEILPANVAGGA 360

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQAR 417
           MALINSMGALGSF GS+LVGYLN  TG PG SYL M GALL++V LT  L P    R
Sbjct: 361 MALINSMGALGSFGGSYLVGYLNSSTGSPGTSYLLMSGALLLSVVLTIFLKPGASDR 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: 861
Number of extensions: 33
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: 430
Length adjustment: 32
Effective length of query: 393
Effective length of database: 398
Effective search space:   156414
Effective search space used:   156414
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:

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