GapMind for catabolism of small carbon sources

 

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

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__Burk376:H281DRAFT_03749
          Length = 360

 Score =  298 bits (762), Expect = 2e-85
 Identities = 174/371 (46%), Positives = 220/371 (59%), Gaps = 22/371 (5%)

Query: 1   MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60
           M  +QL+ + KR+GDT  V  + L IDD EF+VLVGPSGCGKST +RM+AGLE  + GD+
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120
            IGG   N   PQ R+I+MVFQ YALYPH++V +NI FG    +  + A    R+   A+
Sbjct: 61  MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKE-SPANFKPRIEAAAK 119

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            L +   LDR P  LSGGQ+QRVA+GRA+VR+P +FL DEPLSNLDAKLR +MRTE++ L
Sbjct: 120 MLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKAL 179

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
             +L  T +YVTH+Q EAMTMADRI VM+ G ++Q+  P E Y  P NLFVA F+G P +
Sbjct: 180 HQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSM 239

Query: 241 NLVRGTRSESTFVGEHFSYPL---DEDVME----SVDDRDDFVLGVRPEDIEVADAAPDD 293
           N   G     T  G   +  L    E V+E    S        LGVRPE IE     P  
Sbjct: 240 NFAEGVLVNRT-QGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTP-- 296

Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPP 353
                 D+ M V VVEP G +     +H       D     T     V  G+RVT+ +P 
Sbjct: 297 ------DVTMQVEVVEPTGAE-----THLYGKIGGDTWCVTTRQRSKVEPGERVTLRLPA 345

Query: 354 DKIHLFDAETG 364
             IHLFD E+G
Sbjct: 346 AHIHLFDTESG 356


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: 378
Number of extensions: 22
Number of successful extensions: 5
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: 360
Length adjustment: 30
Effective length of query: 353
Effective length of database: 330
Effective search space:   116490
Effective search space used:   116490
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: 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