GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Burkholderia phytofirmans PsJN

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>FitnessBrowser__BFirm:BPHYT_RS17470
          Length = 362

 Score =  301 bits (771), Expect = 2e-86
 Identities = 166/357 (46%), Positives = 224/357 (62%), Gaps = 24/357 (6%)

Query: 1   MAGIKIDKINKFYGTTQ-ALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59
           MA + +  + K Y   Q  L  I++D+ DGEFVV VGPSGCGKSTLLR +AGLE +S G 
Sbjct: 1   MAALTLQGVKKTYDGKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEGS 60

Query: 60  IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119
           I I G+ V  +EP DR++AMVFQ+YALYPHM+V ENM + +K+ G +     +R+  AA+
Sbjct: 61  ISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAAQ 120

Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179
           +L+LE  L RKP +LSGGQRQRVA+GRAIV+ P+VFLFDEPLSNLDA+LRVQMR+E++ L
Sbjct: 121 ILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180

Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239
           H +L  T +YVTHDQ+EAMT+A +++V+N+G  EQ+G+P ++Y +P + FVA FIGSP M
Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPGM 240

Query: 240 NVFSSDVG----------------LQDI-SLDASAA-----FVGCRPEHIEIVPDGDGHI 277
           N+    V                 L D+ S+    A      +G RPEH+        H 
Sbjct: 241 NLLEGRVSDDGAFFEVAGNGPKLPLTDVASIGREVARGREWTLGIRPEHMSPGQADAPHA 300

Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEA 334
             TV   E LG ++L + G  G   +  R+        G A+ +      LH FD A
Sbjct: 301 TLTVDSCELLGADNLAH-GRWGKHDVTVRLPHAHRPAAGEALQVALPARHLHFFDPA 356


Lambda     K      H
   0.320    0.139    0.396 

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: 349
Number of extensions: 14
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: 338
Length of database: 362
Length adjustment: 29
Effective length of query: 309
Effective length of database: 333
Effective search space:   102897
Effective search space used:   102897
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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