GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Paraburkholderia bryophila 376MFSha3.1

Align Inositol transport system permease protein (characterized)
to candidate H281DRAFT_04148 H281DRAFT_04148 monosaccharide ABC transporter membrane protein, CUT2 family

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



>FitnessBrowser__Burk376:H281DRAFT_04148
          Length = 335

 Score =  231 bits (589), Expect = 2e-65
 Identities = 135/308 (43%), Positives = 188/308 (61%), Gaps = 18/308 (5%)

Query: 33  IGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLAL 92
           IGL+      +    SFL  +  +  ++ QVSI  ++A+G+T VI+T GIDLS GSV+AL
Sbjct: 41  IGLLVVCIVMVFASDSFLSGAN-IENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMAL 99

Query: 93  SAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIAT 152
           +  +AA L             +  +     +A+G+ VGL  GA NG  +A  G+PP I T
Sbjct: 100 AGTLAAGLM------------VAGMNALAALAVGVAVGLGFGAANGFFVAFAGMPPIIVT 147

Query: 153 LGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVIIFLVVAVIFHIALRYTK 207
           L  M  ARGLA  YT G P+  L D  +  G G +     PV+I  V+ VI  + L    
Sbjct: 148 LATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGIQAPVVIMAVIYVIAWVLLERMP 207

Query: 208 YGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYE 267
           +G+Y YAIGGN QA R SG+ V R  +IVY+IAGL +  A +V +AR  +GQ   G+ +E
Sbjct: 208 FGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSSFAAIVLTARLMSGQPNAGVGFE 267

Query: 268 LDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAV 327
           LDAIAA V+GGTS++GG G I GT+IGAL+LGV+ +G   VGV+ Y+Q++IKG II++A+
Sbjct: 268 LDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAI 327

Query: 328 VIDQYRNK 335
            I + R K
Sbjct: 328 YISRDRRK 335


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: 282
Number of extensions: 10
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: 340
Length of database: 335
Length adjustment: 28
Effective length of query: 312
Effective length of database: 307
Effective search space:    95784
Effective search space used:    95784
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.

Links

Downloads

Related tools

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