GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11895 in Pseudomonas simiae WCS417

Align Inositol transport system permease protein (characterized)
to candidate GFF2674 PS417_13640 ribose ABC transporter permease

Query= reanno::WCS417:GFF2333
         (340 letters)



>lcl|FitnessBrowser__WCS417:GFF2674 PS417_13640 ribose ABC
           transporter permease
          Length = 325

 Score =  210 bits (534), Expect = 5e-59
 Identities = 124/305 (40%), Positives = 184/305 (60%), Gaps = 19/305 (6%)

Query: 35  LVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSA 94
           L+  L G+ +  ++FL   Q L ++  Q S+  +LA G+T VI+T GIDLS G++LA SA
Sbjct: 28  LILLLVGFALASENFL-TMQNLSIISQQASVNVVLAAGMTFVILTAGIDLSVGAILAASA 86

Query: 95  MIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLG 154
           ++A   + +  F                +A G+G GLL G +NG +IA   +PPFI TLG
Sbjct: 87  VVALQASMSPQFGM------------FGIAAGIGFGLLLGLVNGGLIAFMRLPPFIVTLG 134

Query: 155 MMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIAL-----RYTKYG 209
            + + RGLAR   + + V      +  IG+ ++  + +LV+  +  +AL     R T  G
Sbjct: 135 ALTAMRGLARLLADDKTVFNPDLPFAFIGNDSLLGVPWLVIIAVAVVALSWFILRRTVMG 194

Query: 210 KYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARA-ATGQAGMGMSYEL 268
              Y++GGN +AAR SGI V + L+ VY+++G LAGL  V++++R  A     +G SYEL
Sbjct: 195 VQIYSVGGNPEAARLSGIKVWKVLLFVYAMSGALAGLGAVMSASRLFAANGLQLGQSYEL 254

Query: 269 DAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVV 328
           DAIAA ++GGTS  GGVG I GT+IGALI+ V+ +G   +GV    Q IIKG++I+ AV 
Sbjct: 255 DAIAAVILGGTSFTGGVGTIGGTLIGALIIAVLTNGLVLLGVSDIWQYIIKGIVIIGAVA 314

Query: 329 IDQYR 333
           +D+YR
Sbjct: 315 LDRYR 319


Lambda     K      H
   0.325    0.140    0.394 

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: 268
Number of extensions: 11
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: 340
Length of database: 325
Length adjustment: 28
Effective length of query: 312
Effective length of database: 297
Effective search space:    92664
Effective search space used:    92664
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 paper from 2022 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