GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate AO356_10420 AO356_10420 polar amino acid ABC transporter permease

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_10420
          Length = 221

 Score =  136 bits (343), Expect = 3e-37
 Identities = 77/216 (35%), Positives = 127/216 (58%), Gaps = 2/216 (0%)

Query: 1   MNYQLNFAAVWRDFDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVY 60
           MN+  ++A +       L  +G+ L++ L++IA   ++ L+ A  L+ +   L+ L  +Y
Sbjct: 1   MNF--DYAFILSTLPAFLKAVGVTLQVGLIAIATSLLVALVNATILVLRTPYLQRLVGLY 58

Query: 61  VTVIRNTPILVLILLIYFALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGL 120
           V + RNTP+L+ +  +YFALP+LGI++    + IIT++   GAYLTEV R G+ ++P+  
Sbjct: 59  VELARNTPLLIQLFFVYFALPALGIKVSGFAAAIITMTFLGGAYLTEVLRAGVDAVPQAQ 118

Query: 121 REAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKI 180
            E+G +IGL   Q+  YV +P      LP+L  NFI L K+T++ +A+AVPE+ Y  +  
Sbjct: 119 LESGRSIGLSHGQLLRYVILPQAGILSLPSLFANFIFLLKETTVVSAVAVPEILYTTKSY 178

Query: 181 NVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRL 216
               Y+  E   V T + V     +++LL  LE+RL
Sbjct: 179 IALYYKTYEMLAVLTLICVLLFLPLSLLLSRLERRL 214


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: 175
Number of extensions: 10
Number of successful extensions: 3
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: 221
Length adjustment: 22
Effective length of query: 198
Effective length of database: 199
Effective search space:    39402
Effective search space used:    39402
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