GapMind for catabolism of small carbon sources

 

Alignments 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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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