GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS03645 in Pseudomonas fluorescens FW300-N2C3

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AO356_23210 AO356_23210 ABC transporter

Query= uniprot:D8IZC8
         (344 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23210 AO356_23210 ABC
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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