GapMind for catabolism of small carbon sources

 

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

Align RhaQ (characterized, see rationale)
to candidate AO356_20255 AO356_20255 arabinose ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20255
          Length = 322

 Score =  152 bits (383), Expect = 1e-41
 Identities = 95/314 (30%), Positives = 159/314 (50%), Gaps = 12/314 (3%)

Query: 21  LRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISG 80
           LRR    W +LL A+   IFV  +L    FL   N+       +   + A  M   + SG
Sbjct: 17  LRRFLDDWVMLLAAIG--IFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASG 74

Query: 81  EIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGT----GLACGVFNGVLVSVLKLPS 136
             DLSV ++IA A    G    + +     V +G+      GL  G+ NG++++ L++ +
Sbjct: 75  HFDLSVGSVIACA----GVVAAVVMRDTNSVFLGVSAALAMGLIVGLINGIVIAKLRVNA 130

Query: 137 IVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAIL 196
           ++ T+ TM + RG++YI    +A G     F  FG G +  V     ++ I   + F  L
Sbjct: 131 LITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQLFGV-PVPILITIACFLFFGWL 189

Query: 197 LHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSI 256
           L+ T +GR   AIG N  AA  +G+ V+R K I+F + G++  +A V L SR+ S +P I
Sbjct: 190 LNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMI 249

Query: 257 AQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGL 316
            QG+EL V++  VLGG+S+ GG    R V +    ++ ++   + L N+      +  G 
Sbjct: 250 GQGFELTVISACVLGGVSLSGGIGMIRHV-IAGVLILAIIENAMNLKNIDTFYQYVIRGS 308

Query: 317 LIIVTIAIPIIARR 330
           ++++ + I  + +R
Sbjct: 309 ILLLAVVIDRLKQR 322


Lambda     K      H
   0.330    0.145    0.423 

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: 279
Number of extensions: 13
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: 337
Length of database: 322
Length adjustment: 28
Effective length of query: 309
Effective length of database: 294
Effective search space:    90846
Effective search space used:    90846
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: 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