GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Burkholderia phytofirmans PsJN

Align Inositol transport system permease protein (characterized)
to candidate BPHYT_RS22740 BPHYT_RS22740 ABC transporter permease

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



>FitnessBrowser__BFirm:BPHYT_RS22740
          Length = 328

 Score =  186 bits (472), Expect = 7e-52
 Identities = 105/304 (34%), Positives = 175/304 (57%), Gaps = 19/304 (6%)

Query: 41  GWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASL 100
           G+ +   S  ++ Q L L++ Q  ++ ++AIG T +++T GIDLS G V+A  ++I    
Sbjct: 35  GFFISQSSRFLSFQNLSLILQQTMVVAVIAIGQTLIVLTGGIDLSCGMVMAFGSIIMTKF 94

Query: 101 AQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSAR 160
           A T             +P  + +  G+G   L GA+NG +I    +P FI TLG +  A 
Sbjct: 95  AVT-----------LGVPPVLAILCGVGASALFGALNGVLITRIKLPAFIVTLGTLNIAF 143

Query: 161 GLARYYTEGQPVSMLSDSYTAIGH----GAMPVIIFLVVAVIFHIA----LRYTKYGKYT 212
            L + Y+  + VS L D+   +G+    G   V    V+ ++ ++A    LR T  G++ 
Sbjct: 144 ALTQIYSNAESVSNLPDAIMFLGNTFKLGPADVTYGTVLTLLMYLATWFVLRDTVPGRHL 203

Query: 213 YAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIA 272
           YA+G N +AAR  G++ ++ L+ VYS+AG + G+A +++ +R   G    G +  LD+I 
Sbjct: 204 YALGNNPEAARLMGLSSQKILLTVYSLAGAIYGIAALLSVSRTGVGDPQAGQTENLDSIT 263

Query: 273 AAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQY 332
           A V+GGTSL GG G I+GT++GALI+GV  +G T +GV +  Q +I G+++++AV  D+ 
Sbjct: 264 AVVLGGTSLFGGRGSISGTLLGALIVGVFRNGLTLIGVSSVYQVLITGMLVILAVAADKL 323

Query: 333 RNKR 336
            ++R
Sbjct: 324 SHRR 327


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: 211
Number of extensions: 10
Number of successful extensions: 2
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: 328
Length adjustment: 28
Effective length of query: 312
Effective length of database: 300
Effective search space:    93600
Effective search space used:    93600
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