GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Shewanella oneidensis MR-1

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 200216 SO1033 iron-compound ABC transporter, ATP-binding protein, putative (NCBI ptt file)

Query= CharProtDB::CH_003736
         (237 letters)



>FitnessBrowser__MR1:200216
          Length = 285

 Score = 82.0 bits (201), Expect = 1e-20
 Identities = 69/224 (30%), Positives = 111/224 (49%), Gaps = 19/224 (8%)

Query: 21  LHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFDDKDITDWQTAKIMRE 80
           L  V+  + +GE++ LIG NGAGK++LL  L    R T G+I    +DI+   + K    
Sbjct: 18  LSGVNFALQRGEMLGLIGPNGAGKSSLLRCLYRFIRPTQGQISLFSQDISQ-LSPKAFAC 76

Query: 81  AVAIVPEGRRVFSRMTVEENLAMG-----GFF-----AERDQFQERIKWVYELFPRLHER 130
            VA+V +    +  MT E+ +AMG     G F      + D+  + ++ V  L  +LH  
Sbjct: 77  KVAVVQQDTPHYFDMTTEQLVAMGLTPHKGMFDSHSSGDSDKIIKALEKV-GLSHKLH-- 133

Query: 131 RIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLREQGMTI 190
             Q+   +SGGE+Q   I RA++  P LL+LDEP+  L    ++     +E +R  G+++
Sbjct: 134 --QQYERLSGGEKQRALIARAIVQQPLLLILDEPTNHLD---VRYQIQILELVRSLGISV 188

Query: 191 FLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAY 234
                + N A  L D   +L+NG V    T   +L  E +   +
Sbjct: 189 IASIHDLNLASALCDSLLLLDNGQVSAMGTPTEVLTEERIAQVF 232


Lambda     K      H
   0.321    0.137    0.390 

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: 171
Number of extensions: 6
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: 237
Length of database: 285
Length adjustment: 24
Effective length of query: 213
Effective length of database: 261
Effective search space:    55593
Effective search space used:    55593
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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