GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pseudomonas fluorescens FW300-N2E3

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate AO353_13360 AO353_13360 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13360
          Length = 238

 Score =  273 bits (699), Expect = 2e-78
 Identities = 145/236 (61%), Positives = 180/236 (76%), Gaps = 2/236 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           +L++  +  FYG I+ALK V + I  GE VSLIG+NGAGKSTLLM+I G PRA  G+I +
Sbjct: 5   ILELKAIDVFYGPIQALKKVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAAGGQIVY 64

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120
            G DIT   ++ +   GIAQSPEGRR+FP M+V ENL MG+I         +++R+  LF
Sbjct: 65  RGVDITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMGTIPIGDQYATEDMQRMFELF 124

Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180
           PRLKER +QRA TMSGGEQQMLAI RALMS+P+LLLLDEPSLGLAP+VVKQIF  ++++ 
Sbjct: 125 PRLKERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFATLREL- 183

Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEGGH 236
               MT+F+VEQNA HALKL+ R YVMVNG++ +SGTG ELL NEEVR+AYL GGH
Sbjct: 184 AGTGMTIFLVEQNANHALKLSDRAYVMVNGEIRLSGTGKELLVNEEVRNAYL-GGH 238


Lambda     K      H
   0.320    0.136    0.377 

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: 220
Number of extensions: 6
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: 236
Length of database: 238
Length adjustment: 23
Effective length of query: 213
Effective length of database: 215
Effective search space:    45795
Effective search space used:    45795
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: 46 (22.3 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