GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Dshi_0546 in Phaeobacter inhibens BS107

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein

Query= reanno::Dino:3607124
         (338 letters)



>lcl|FitnessBrowser__Phaeo:GFF729 PGA1_c07440 ABC transporter, ATP
           binding protein
          Length = 353

 Score =  368 bits (944), Expect = e-106
 Identities = 194/350 (55%), Positives = 243/350 (69%), Gaps = 19/350 (5%)

Query: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60
           M G+ + K  K YG  Q + D++L I+DGEF VFVGPSGCGKSTLLR +AGLE  SSG I
Sbjct: 1   MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60

Query: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120
            IG RDVT ++ ADR +AMVFQSYALYPHMTV +NM FG+K+NG   +  +E++AEA+R+
Sbjct: 61  HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120

Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180
           L+L+DYL RKP  LSGGQRQRVAIGRAIV+ P VFLFDEPLSNLDA+LRV MRVE+  LH
Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180

Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240
           K++GATMIYVTHDQVEAMT+ADKIVVL  GR+EQVGSPM+LY  P++RFVA FIGSP+MN
Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSMN 240

Query: 241 VFSSDV--------GLQD--------ISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVK 284
                V         L++        +  D S   +G RP+H+ +        +  + ++
Sbjct: 241 FLEGTVQGDGVVVPALENRRVATSVALPADGSKVLLGLRPQHLSVTA---ADSSLVLDLR 297

Query: 285 ERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEA 334
           ERLGG S  YL    G +++    GD+    G AV+L F     + FD A
Sbjct: 298 ERLGGVSYDYLSTPTGEKLIVETRGDEALPEGTAVALGFDDADAYIFDGA 347


Lambda     K      H
   0.320    0.139    0.396 

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: 384
Number of extensions: 14
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: 338
Length of database: 353
Length adjustment: 29
Effective length of query: 309
Effective length of database: 324
Effective search space:   100116
Effective search space used:   100116
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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