GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Marivita geojedonensis DPG-138

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

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



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  365 bits (936), Expect = e-105
 Identities = 195/346 (56%), Positives = 244/346 (70%), Gaps = 18/346 (5%)

Query: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60
           M+G+ ++ + K YG TQ +  ++LD++DGEF VFVGPSGCGKSTLLR +AGLE  + G I
Sbjct: 1   MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60

Query: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120
            IGGRDVT ++P+DR ++MVFQ+YALYPHMTV ENM FG+K+ G      KE++AEA+R+
Sbjct: 61  RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRI 120

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

Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240
           K++GATMIYVTHDQVEAMT+ADKIVVL  GRIEQVG+PM+LY  P++RFVA FIGSP+MN
Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMN 240

Query: 241 VFS---------SDVGLQDISLDASA-----AFVGCRPEHIEIVPDGDGHIAATVHVKER 286
                       SD  +  +S  ASA       +G RPEH+E+ P G  H    V + E 
Sbjct: 241 FIRGRVQGGEVVSDGLVHSVSKTASAQEGQEVLIGLRPEHLELRP-GSSH---RVDLTES 296

Query: 287 LGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD 332
           LGG S  +L    G +I+    GD  +  G  V L      +  FD
Sbjct: 297 LGGVSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFD 342


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: 398
Number of extensions: 18
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: 350
Length adjustment: 29
Effective length of query: 309
Effective length of database: 321
Effective search space:    99189
Effective search space used:    99189
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 24 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