GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Pseudomonas fluorescens FW300-N2E2

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Pf6N2E2_524 Inositol transport system permease protein

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524
          Length = 340

 Score =  209 bits (531), Expect = 1e-58
 Identities = 134/324 (41%), Positives = 199/324 (61%), Gaps = 28/324 (8%)

Query: 35  LPVLVVLYLLFYGLTLYLSGDG-----TSNFASAENTMNILRQVAINLVLAAGMTFVILT 89
           LP  + ++L+  G+ L     G      S   +++  + ++ QV+I  +LA G+T VI+T
Sbjct: 20  LPTELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIIT 79

Query: 90  AGIDLSVGSVLAVSAVLGMQV------------SLGAAPGWAIPMF--IFSGLVMGMVNG 135
            GIDLS GSVLA+SA++   +            SL   P W IP+   +  GL+ G +NG
Sbjct: 80  TGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW-IPVVAGLGVGLLAGAING 138

Query: 136 AMVALLNINAFVVTLGTMTAFRGAAYLLADGTTV-LNNDIPSFEWIGNGDFLHVPWLIWV 194
           +++A+  I  F+ TLG M + RG A    +G  V + +D  S+  IG+G    +P +I++
Sbjct: 139 SIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSD--SYTAIGHGA---MPVIIFL 193

Query: 195 AVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMS 254
            VAV+    + LR T  G + YAIGGN+QAAR +GI V   L+ VYSI+GL +GLAG ++
Sbjct: 194 VVAVIF--HIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVA 251

Query: 255 ASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLS 314
           ++R        G  YELDAIAA V+GGTSL GGVG I GTV+GALI+GVM +G T +G+ 
Sbjct: 252 SARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVD 311

Query: 315 SFWQYVAKGAVIVLAVILDKWRQK 338
           ++ Q + KG +IV+AV++D++R K
Sbjct: 312 AYIQDIIKGLIIVVAVVIDQYRNK 335


Lambda     K      H
   0.324    0.138    0.417 

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: 323
Number of extensions: 16
Number of successful extensions: 4
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: 344
Length of database: 340
Length adjustment: 29
Effective length of query: 315
Effective length of database: 311
Effective search space:    97965
Effective search space used:    97965
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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