GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Burkholderia phytofirmans PsJN

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate BPHYT_RS29175 BPHYT_RS29175 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__BFirm:BPHYT_RS29175
          Length = 390

 Score =  263 bits (673), Expect = 5e-75
 Identities = 156/366 (42%), Positives = 215/366 (58%), Gaps = 20/366 (5%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           + + +LT + G    +++L LD+   EF+VL+GPSGCGKST L  +AGL   T G I I 
Sbjct: 37  VAVRNLTIQLGANTVIENLDLDVQAGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIA 96

Query: 64  GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123
           G+ M +  P++R IA+VFQ YALYP M+V +N+ F L    G   AE   RV   +E L 
Sbjct: 97  GEDMTWADPKDRRIALVFQSYALYPTMSVERNLSFALRIN-GTPKAEIARRVARASEMLQ 155

Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183
           +  LL RKP +LSGGQ+QRVA+GRAIVR+ +VFL DEPLSNLDAKLR E+R EL+ L  +
Sbjct: 156 LGPLLKRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQR 215

Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243
           L  T +YVTH+Q EAMT+A R+AVM  G +QQ  +P E Y  P+NLFVA F+G P +NL+
Sbjct: 216 LGATMIYVTHDQVEAMTLATRMAVMRGGVIQQFGTPAEVYARPDNLFVATFLGTPAMNLI 275

Query: 244 RG---TRSEST-FVGEHFSYPLDEDVMESVDDRD-DFVLGVRPEDIEVADAAPDDAALDD 298
           +G   TR  +  F  EH+   +      +        VLGVR ED+ +A+ A + A    
Sbjct: 276 KGRLETRDGALHFCTEHWRLDVSRYPFRTTPANGLPCVLGVRAEDVRLAEGASEHA---- 331

Query: 299 HDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHL 358
                 V++VEP G+  V+ L +     A     ++ +    +  GD    +     + L
Sbjct: 332 -----KVSLVEPMGNHRVIWLDYHGVQVA-----SIDQTKTPLAIGDAAAFSFDSTHVSL 381

Query: 359 FDAETG 364
           FD   G
Sbjct: 382 FDEAGG 387


Lambda     K      H
   0.317    0.135    0.386 

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: 347
Number of extensions: 11
Number of successful extensions: 3
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: 390
Length adjustment: 30
Effective length of query: 353
Effective length of database: 360
Effective search space:   127080
Effective search space used:   127080
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: 41 (21.6 bits)
S2: 50 (23.9 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