GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2674
          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:

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