Aligments for a candidate for kguT in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for kguT in Burkholderia phytofirmans PsJN

Align KguT (characterized, see rationale)
to candidate BPHYT_RS10985 BPHYT_RS10985 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__BFirm:BPHYT_RS10985
          Length = 432

 Score =  560 bits (1444), Expect = e-164
 Identities = 267/420 (63%), Positives = 326/420 (77%), Gaps = 2/420 (0%)

Query: 6   LAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFF 65
           +AP+RWWY+MPI+FITYSLAYLDRANYGFAAA+G+  DL IT   SSL+G+LFFLGY  F
Sbjct: 7   VAPQRWWYLMPIIFITYSLAYLDRANYGFAAAAGIDRDLGITHGTSSLIGSLFFLGYCLF 66

Query: 66  QVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLI 125
           QVPGAIYA++ SVKKLIF SLILWG  A  TGMV ++ +L+ +RF+LGVVEAAVMP+ML+
Sbjct: 67  QVPGAIYAQRNSVKKLIFFSLILWGLCAAATGMVSNIPMLMMLRFVLGVVEAAVMPSMLM 126

Query: 126 YLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIW 185
           Y+  WFTR+ERSRANTFLILGNPVT+LWMSVVSGYLV+ F WR MF+ EG PA++WA +W
Sbjct: 127 YISRWFTRSERSRANTFLILGNPVTVLWMSVVSGYLVRSFGWREMFVFEGAPALIWAVVW 186

Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSI 245
           W  V DRP  A W+ A EKT L   L AEQ  I PV++Y+ AFRS  V+     +  WSI
Sbjct: 187 WFTVKDRPADAPWMSAAEKTELDARLKAEQAHIAPVRDYKAAFRSSIVLKFCAIHALWSI 246

Query: 246 GVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305
           GVYGF++WLPSILK A+ +DIV+ GWL+AVPYL A++ ML  SW SD+ + RK FVWP L
Sbjct: 247 GVYGFIMWLPSILKAASTIDIVSVGWLAAVPYLAAIILMLLASWLSDKTRNRKLFVWPLL 306

Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365
           L+  +AF  SY++G  HFW S+ LLV+AGA MYAPYGPFFA+VPEL+P NV GGA+ LIN
Sbjct: 307 LVGTIAFVASYLIGGSHFWISFALLVVAGATMYAPYGPFFALVPELIPGNVLGGAIGLIN 366

Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVAL--TAVLNPSQQARRQQLAP 423
           + GALG+F+GSW+VGYLNGVTG P ASY+FM G LL +V L  T   N  + A+R    P
Sbjct: 367 ACGALGAFAGSWVVGYLNGVTGSPAASYIFMAGGLLSSVILMITVPANSDEHAKRGAALP 426


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: 777
Number of extensions: 35
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources