GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Rhodobacter viridis JA737

Align Inositol transport system permease protein (characterized)
to candidate WP_110806514.1 C8J30_RS14100 ABC transporter permease

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



>NCBI__GCF_003217355.1:WP_110806514.1
          Length = 339

 Score =  402 bits (1033), Expect = e-117
 Identities = 201/323 (62%), Positives = 251/323 (77%)

Query: 18  RRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVI 77
           RRLP E++I  VL+GI LVFE+ GWI + QSFLM+  RL +MILQVS+IG++++GVTQVI
Sbjct: 16  RRLPPEVNILFVLVGIALVFEILGWIFQGQSFLMSIDRLKIMILQVSVIGIISVGVTQVI 75

Query: 78  ITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAIN 137
           I  GIDLSSGSV+   AM A S AQ S ++RAV+P LTDLP  +P+A+GL  G L G IN
Sbjct: 76  IAGGIDLSSGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPAIVPIALGLMAGALVGLIN 135

Query: 138 GSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVIIFLVVAV 197
           G++IA   IPPFIATLG MV+ARG A++YT+GQP+S  +D +  IG G MPV IFL VA 
Sbjct: 136 GALIAYAKIPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFIGKGMMPVAIFLAVAA 195

Query: 198 IFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAAT 257
           IFH+A++YT+YGK+TYAIG N QAAR SGINV+ HLI VY +A  LA LAG+V +AR  T
Sbjct: 196 IFHVAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAATLAALAGMVVAARGQT 255

Query: 258 GQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDI 317
            QAGMG++YELDAIA AVIGG SL GG G I GT+IG +I GV+ SGFTF+ +DAY Q++
Sbjct: 256 AQAGMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIFGVIISGFTFLRLDAYYQEM 315

Query: 318 IKGLIIVVAVVIDQYRNKRKLKR 340
           IKG+IIV AVV D YR K++ K+
Sbjct: 316 IKGVIIVAAVVADVYRQKKRTKK 338


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: 367
Number of extensions: 10
Number of successful extensions: 1
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: 339
Length adjustment: 28
Effective length of query: 312
Effective length of database: 311
Effective search space:    97032
Effective search space used:    97032
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 24 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