GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas fluorescens FW300-N2E3

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate AO353_25130 AO353_25130 ABC transporter

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25130
          Length = 381

 Score =  332 bits (850), Expect = 1e-95
 Identities = 177/355 (49%), Positives = 228/355 (64%), Gaps = 25/355 (7%)

Query: 20  LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79
           L+L  + K  G   +L+ + L++  GEFV+FVGPSGCGKSTLLR IAGL+   +G + ID
Sbjct: 4   LKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDLLID 63

Query: 80  GVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSL 139
              V  + P +RG+ MVFQSYALYPH++V DN+  GLK A   K+ + E+V + A +L L
Sbjct: 64  ERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQILQL 123

Query: 140 EPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSL 199
           +  L R+P ELSGGQRQRVA+GRA+ REP + LFDEPLSNLDA+LRV  R EIARLH  L
Sbjct: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHARL 183

Query: 200 KATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFIE 259
            +TMIYVTHDQVEAMTLADKIVVLN GR+EQVGSP ELY RPA+ FVAGF+GSP+MNF+ 
Sbjct: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLA 243

Query: 260 AAKLGDGEAK-------------------------TIGIRPEHIGLSRESGDWKGKVIHV 294
           A     GE                           ++G+RPEH+ L    G     V  V
Sbjct: 244 ARLHAPGETSLVDTPVLGMTSLPFDSSNLAADTPLSLGVRPEHVSLKAADGTVGVIVTGV 303

Query: 295 EHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFDADGRVIK 349
           E+LG++T +++++     L  R      +   D V     IG++H FDADG  ++
Sbjct: 304 EYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFDADGTALR 358


Lambda     K      H
   0.320    0.137    0.393 

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: 399
Number of extensions: 10
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: 352
Length of database: 381
Length adjustment: 30
Effective length of query: 322
Effective length of database: 351
Effective search space:   113022
Effective search space used:   113022
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