GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Paraburkholderia bryophila 376MFSha3.1

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Burk376:H281DRAFT_05701
          Length = 362

 Score =  302 bits (773), Expect = 1e-86
 Identities = 174/369 (47%), Positives = 229/369 (62%), Gaps = 17/369 (4%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA LTL  V K Y     G    +  I +D++DGEF+V+VGPSGCGKST LRM+AGLE +
Sbjct: 1   MAALTLQGVKKTYD----GKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERI 56

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           +EG + +  +V+N +  +DR+IAMVFQ+YALYPH SV  NM + L+ + G+   +I QRV
Sbjct: 57  SEGTISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIA-GVDRAQIAQRV 115

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
                +L +  LL RKP +LSGGQ+QRVA+GRAIVR+P VFL DEPLSNLDA+LR +MR 
Sbjct: 116 NAAAQILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRL 175

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+QRL   L  T++YVTHDQ EAMT+  RV V++ G  +Q+G P + Y RP  +FVAGFI
Sbjct: 176 EIQRLHARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFI 235

Query: 241 GEPSMNLFDGSLS--GDTF--RGDGFDYPLSGATRDQLGGASG--LTLGIRPEDVTVGER 294
           G P MNL +G +S  G TF   G+G   PL+G        A G   TLGIRPE ++ G+ 
Sbjct: 236 GSPGMNLLEGRVSDDGSTFDVAGNGPQLPLAGVASIGREVAKGREWTLGIRPEHMSPGQA 295

Query: 295 RSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDA 354
            +   T   +    E  G +N  H R+   D     TA      R  AG+   V+ P   
Sbjct: 296 DAPHTTLTVD--SCELLGADNLAHGRWGKHD----VTARLPHAHRPAAGEALQVALPARH 349

Query: 355 IHLFDGETG 363
           +H FD  +G
Sbjct: 350 LHFFDPASG 358


Lambda     K      H
   0.316    0.136    0.384 

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: 382
Number of extensions: 21
Number of successful extensions: 4
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: 383
Length of database: 362
Length adjustment: 30
Effective length of query: 353
Effective length of database: 332
Effective search space:   117196
Effective search space used:   117196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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