GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Phaeobacter inhibens BS107

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= uniprot:D4GP38
         (383 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  289 bits (740), Expect = 7e-83
 Identities = 171/369 (46%), Positives = 234/369 (63%), Gaps = 29/369 (7%)

Query: 1   MGQIQLTDLTKRFGDTV-AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59
           M Q+ L  + K + + V AV   S  I+D EF+VLVGPSGCGKST LRM+AGLE  T G 
Sbjct: 1   MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60

Query: 60  IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119
           + IG   +N   P +RDIAMVFQ+YALYPHMTVR+NI +GL+  +    AE  ++V E A
Sbjct: 61  LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKT-PEAEIKQKVAEAA 119

Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179
           + L + + LDRKP +LSGGQ+QRVA+GRAIVRDP +FL DEPLSNLDAKLR +MR E++ 
Sbjct: 120 KMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKA 179

Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239
           LQ +L VT++YVTH+Q EAMTMADRI V++ G ++Q+ +P E YH P ++FVA F+G P 
Sbjct: 180 LQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPP 239

Query: 240 INLVRGTRSESTFVGEHFSYPLDEDVMESVDD--RDDFVLGVRPEDIEVADAAPDDAALD 297
           +NL+     ++T      + P D   M ++D   +    LG+RPED+++         + 
Sbjct: 240 MNLL-----DATIANGQVTLP-DGVSMGALDTSAQGAVKLGIRPEDVQL---------VA 284

Query: 298 DHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQ--AVTEGMHLVTRGDRVTVTIPPDK 355
           +  L +DV ++E  G   +LH     QP     L+   V  G H         +++ P  
Sbjct: 285 EGGLAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPGTH--------QISVDPAA 336

Query: 356 IHLFDAETG 364
           I LFDAE+G
Sbjct: 337 ICLFDAESG 345


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: 371
Number of extensions: 12
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: 348
Length adjustment: 30
Effective length of query: 353
Effective length of database: 318
Effective search space:   112254
Effective search space used:   112254
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