GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Burkholderia phytofirmans PsJN

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS31940 BPHYT_RS31940 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__BFirm:BPHYT_RS31940
          Length = 294

 Score =  141 bits (356), Expect = 2e-38
 Identities = 90/299 (30%), Positives = 152/299 (50%), Gaps = 15/299 (5%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M   VQ  LN L  GS+Y L A+G T+++G++G++NFAHG  F LG     ++   L   
Sbjct: 1   MALIVQLALNTLQAGSVYVLFALGLTLIFGVMGVVNFAHGQFFTLGALLTSVLVPALREA 60

Query: 61  FAGLPVAVLLL----VMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLS 116
           F G+ VA+       + +V  + + +L      R   R   GSF     I ++G+ +   
Sbjct: 61  F-GMGVALAFTFASAISIVAVLALAALVYQFGFRHYLRDTVGSF-----ILSVGLLLFFE 114

Query: 117 NFIQVTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQ 176
                  G   + +P +     +    ++ L+++++  I  ++  + + ++  T  GRA 
Sbjct: 115 GVFLWVFGGVPRVVPNIAPGELRVFGAAIELQRLVVFAIAVIITVLLYLMLAFTRFGRAI 174

Query: 177 RATEQDRKMAALLGVNVDQTISITFVMGAALAAVAG--TMYLMYYGVASFNDGFTPGVKA 234
           RAT  D   A L G+   +T+   F++G+ L+AV+G  T  +     A  ND     +K 
Sbjct: 175 RATADDAGAATLQGIRDKRTLLYGFMVGSFLSAVSGCLTAPIAVITPAVGNDYL---IKG 231

Query: 235 FTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILG 293
           F   ++GG+GS+PGA+FGGL I LIES+   YF      +  F ++A +L+ +P G+LG
Sbjct: 232 FITIIIGGLGSVPGAIFGGLTIALIESVVGYYFDGTMATIGMFCVVALLLLIRPQGMLG 290


Lambda     K      H
   0.329    0.143    0.421 

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: 286
Number of extensions: 17
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: 300
Length of database: 294
Length adjustment: 26
Effective length of query: 274
Effective length of database: 268
Effective search space:    73432
Effective search space used:    73432
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: 48 (23.1 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