GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate PfGW456L13_878 amino acid ABC transporter, permease protein

Query= reanno::pseudo3_N2E3:AO353_21715
         (220 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_878
          Length = 222

 Score =  132 bits (332), Expect = 5e-36
 Identities = 74/219 (33%), Positives = 119/219 (54%)

Query: 1   MNYQLNFAAVWRDFDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVY 60
           M YQ +F  V  + D LL G    LEL  +   +G  +G++ A       R    + +VY
Sbjct: 1   MAYQFDFLPVVNNTDLLLRGALFTLELTAIGAVLGVGLGIVGALVRAWNIRPFAGIFAVY 60

Query: 61  VTVIRNTPILVLILLIYFALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGL 120
           V +IRNTP LV +  I+F LPSLG+++ +  + ++ + +  GAY TE+ R G+ +IP+G 
Sbjct: 61  VELIRNTPFLVQLFFIFFGLPSLGVQISEWQAAVLAMVINLGAYSTEIIRAGIQAIPRGQ 120

Query: 121 REAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKI 180
            EA  A+ +  ++   +V +   L  V PALS+  I +   +++ + IA  EL++ A  I
Sbjct: 121 LEAAAALAMTRFEAFRHVVLLPALGKVWPALSSQIIIVMLGSAVCSQIATEELSFAANFI 180

Query: 181 NVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRLAIR 219
              ++R  ET+ +TT LY+    LI  LL +L  R   R
Sbjct: 181 QSRNFRAFETYALTTLLYLCMALLIRQLLNWLGHRFIAR 219


Lambda     K      H
   0.329    0.143    0.416 

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: 135
Number of extensions: 4
Number of successful extensions: 1
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: 220
Length of database: 222
Length adjustment: 22
Effective length of query: 198
Effective length of database: 200
Effective search space:    39600
Effective search space used:    39600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 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