GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Dshi_0546 in Pseudomonas stutzeri RCH2

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

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



>lcl|FitnessBrowser__psRCH2:GFF857 Psest_0871 ABC-type sugar
           transport systems, ATPase components
          Length = 371

 Score =  314 bits (805), Expect = 2e-90
 Identities = 176/359 (49%), Positives = 224/359 (62%), Gaps = 22/359 (6%)

Query: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60
           MA + +  I K Y  T     I+LDIEDGEFVVFVGPSGCGKSTLLR +AGLE ++SG +
Sbjct: 1   MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60

Query: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120
            I  + V  + P DR + MVFQSYALYPHMTV ENM FG+K+   +    K R+   A +
Sbjct: 61  LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120

Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180
           LQL+  L+RKP  LSGGQRQRVAIGR +V+ P VFLFDEPLSNLDA LRVQMR+E+  LH
Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180

Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240
           +++ +TMIYVTHDQVEAMT+ADKIVVLN G I QVG P+ LYH P +RFVA F+GSP MN
Sbjct: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240

Query: 241 ---VFSSDVGLQDISLDASAAF------------------VGCRPEHIEIVPDGDGHIAA 279
              V +     + ++++  + +                  +G RPEH  +  + D     
Sbjct: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300

Query: 280 TVHVKERLGGESLLYLGLKGGGQIVAR-VGGDDETKVGAAVSLRFSRHRLHQFDEAGRA 337
            + V ERLG  +LLYL L+    ++   V G+     G   +      + H F E G A
Sbjct: 301 QITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGEA 359


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: 390
Number of extensions: 11
Number of successful extensions: 2
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: 371
Length adjustment: 29
Effective length of query: 309
Effective length of database: 342
Effective search space:   105678
Effective search space used:   105678
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 preprint 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