GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Burkholderia phytofirmans PsJN

Align ABC transporter (characterized, see rationale)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__BFirm:BPHYT_RS17470
          Length = 362

 Score =  329 bits (844), Expect = 6e-95
 Identities = 179/355 (50%), Positives = 238/355 (67%), Gaps = 5/355 (1%)

Query: 1   MIKLKLDNVNKQLGGMR-ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59
           M  L L  V K   G + +L  + +++A GEFVV VGPSGCGKSTLLR++AGL+ I  G 
Sbjct: 1   MAALTLQGVKKTYDGKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEGS 60

Query: 60  LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119
           + I G+ VN LEP++R + MVFQ+YALYPHMSV +N+ + LK+A  D+  + +RV   AQ
Sbjct: 61  ISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAAQ 120

Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179
           IL+L+ LLQRKP+ELSGGQRQRVAMGRA+ REP + LFDEPLSNLDA LRVQMR EI RL
Sbjct: 121 ILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180

Query: 180 HDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRM 239
           H RL +T +YVTHDQ+EAMTLA +++V+N G  EQ+G+P E+YERPA+ FVA F+GSP M
Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPGM 240

Query: 240 NFLSARLQTPGETSLV--DTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGT-A 296
           N L  R+   G    V  +     +T +      +A G   +LGIRPEH+S   AD   A
Sbjct: 241 NLLEGRVSDDGAFFEVAGNGPKLPLTDVASIGREVARGREWTLGIRPEHMSPGQADAPHA 300

Query: 297 GVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFD 351
            + V + E LG++   H   G+ +  + R   +    AG+ +++ L   +LH FD
Sbjct: 301 TLTVDSCELLGADNLAHGRWGKHDVTV-RLPHAHRPAAGEALQVALPARHLHFFD 354


Lambda     K      H
   0.320    0.137    0.394 

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: 374
Number of extensions: 15
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: 381
Length of database: 362
Length adjustment: 30
Effective length of query: 351
Effective length of database: 332
Effective search space:   116532
Effective search space used:   116532
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