GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Burkholderia phytofirmans PsJN

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease

Query= SwissProt::P37772
         (331 letters)



>FitnessBrowser__BFirm:BPHYT_RS16055
          Length = 335

 Score =  149 bits (377), Expect = 7e-41
 Identities = 111/312 (35%), Positives = 163/312 (52%), Gaps = 13/312 (4%)

Query: 2   IKRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGI 61
           +KR+      IG+ V+  +        F S   I N+L   +   IIAVGMT VIL+GGI
Sbjct: 31  LKRSTLFYPFIGLLVVCIVMVFAS-DSFLSGANIENVLRQVSINAIIAVGMTCVILTGGI 89

Query: 62  DLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITL 121
           DLSVGSV+A  G   A ++   G++ + A  + + +G  FGA  G  +    +P  I+TL
Sbjct: 90  DLSVGSVMALAGTLAAGLMVA-GMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTL 148

Query: 122 AGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRL---SAMGLLMLAVVVIGIF 178
           A M   RG++ L+     PI+  + D +S       G G++    A  ++M  + VI   
Sbjct: 149 ATMGIARGLA-LIYTGGYPIDG-LPDWVSFF-----GSGKILGVQAPVVIMAVIYVIAWV 201

Query: 179 LAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYAL 238
           L  R  FG  VYAIGGN  +  L G+      + +Y ++   +  A IV +    +G   
Sbjct: 202 LLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPN 261

Query: 239 AGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIG 298
           AGVG ELDAIA+VV+GGT +SGG G+++GTL G  + G++   +N  G        I  G
Sbjct: 262 AGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGG 321

Query: 299 -ILLFIFIALQR 309
            ILL I+I+  R
Sbjct: 322 IILLAIYISRDR 333


Lambda     K      H
   0.329    0.145    0.428 

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: 342
Number of extensions: 29
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: 331
Length of database: 335
Length adjustment: 28
Effective length of query: 303
Effective length of database: 307
Effective search space:    93021
Effective search space used:    93021
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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