GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate PfGW456L13_3607 Amino acid ABC transporter, permease protein

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3607
          Length = 281

 Score =  135 bits (340), Expect = 8e-37
 Identities = 68/202 (33%), Positives = 122/202 (60%), Gaps = 1/202 (0%)

Query: 11  GVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLV 70
           G    L GA +T+ +   S+ L  ++G +  + RL+ +  V + + + Y +  RGTPLL+
Sbjct: 70  GPDGFLQGAALTLFLCFCSIWLSLLLGFVTALARLS-RSAVAFGVASFYASFFRGTPLLI 128

Query: 71  QLFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSS 130
           Q+ +++ GLPQ G++  A   G+I L +  GAY+SE+ R  I ++  GQ EAA ++G+  
Sbjct: 129 QILLIYLGLPQLGVVPGAISAGIIALSLNYGAYLSEIFRAGIMAVAPGQREAAMALGLGP 188

Query: 131 GLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVY 190
                 +VLPQA+  +IPP  ++FI+++K+S+L+S++ + ++M   Q     SYR +E+ 
Sbjct: 189 VATFLHIVLPQAMRTIIPPTTSQFISMLKDSSLISVMGVWEVMFLAQSYGRSSYRYIEML 248

Query: 191 LAIAVVYFILTGATTLVLRRIE 212
              AV+Y++L+    L+  R+E
Sbjct: 249 TTAAVIYWLLSIGLELIQNRLE 270


Lambda     K      H
   0.328    0.143    0.412 

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: 156
Number of extensions: 5
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: 222
Length of database: 281
Length adjustment: 24
Effective length of query: 198
Effective length of database: 257
Effective search space:    50886
Effective search space used:    50886
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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