GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate AO353_25130 AO353_25130 ABC transporter

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



>FitnessBrowser__pseudo3_N2E3:AO353_25130
          Length = 381

 Score =  320 bits (820), Expect = 4e-92
 Identities = 174/358 (48%), Positives = 231/358 (64%), Gaps = 21/358 (5%)

Query: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60
           M  +K+D +NK  G  + L D++L+I  GEFVVFVGPSGCGKSTLLR +AGL+ + +G +
Sbjct: 1   MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60

Query: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120
            I  R V  +EP +R + MVFQSYALYPHM+V +N+ FG+K+   E    +ER+   A++
Sbjct: 61  LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120

Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180
           LQL+  L RKP +LSGGQRQRVA+GRA+ + P + LFDEPLSNLDA LRVQMR E+  LH
Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180

Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240
            +LG+TMIYVTHDQVEAMT+ADKIVVLN GR+EQVGSP +LY +P SRFVA F+GSP MN
Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240

Query: 241 VFSSD--------------VGLQDISLDAS------AAFVGCRPEHIEIVPDGDGHIAAT 280
             ++               +G+  +  D+S         +G RPEH+ +    DG +   
Sbjct: 241 FLAARLHAPGETSLVDTPVLGMTSLPFDSSNLAADTPLSLGVRPEHVSL-KAADGTVGVI 299

Query: 281 VHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338
           V   E LG E+ ++L       ++ R   +   +VG  V L+     LH FD  G A+
Sbjct: 300 VTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFDADGTAL 357


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: 391
Number of extensions: 13
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: 381
Length adjustment: 29
Effective length of query: 309
Effective length of database: 352
Effective search space:   108768
Effective search space used:   108768
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:

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