GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Shewanella sp. ANA-3

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 7026138 Shewana3_3280 ABC transporter related (RefSeq)

Query= CharProtDB::CH_003736
         (237 letters)



>FitnessBrowser__ANA3:7026138
          Length = 326

 Score = 85.1 bits (209), Expect = 2e-21
 Identities = 69/220 (31%), Positives = 106/220 (48%), Gaps = 11/220 (5%)

Query: 21  LHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFDDKDITDWQTAKIMRE 80
           L E+S  + QGE++ LIG NGAGK++LL  L    R   G I    +DI++  + K    
Sbjct: 36  LSEISFALPQGEMLGLIGPNGAGKSSLLRCLYRFIRPAKGHISLFSQDISE-LSPKAFAC 94

Query: 81  AVAIVPEGRRVFSRMTVEENLAMG-----GFFAERDQFQ-ERIKWVYELFPRLHERRIQR 134
            VA+V +    +  MT E+ +AMG     G F        E+I    E     H+   Q+
Sbjct: 95  KVAVVQQDTPQYFDMTTEQLVAMGLTPHKGMFDTNSSGDGEKIAKALEKVGLSHKVH-QQ 153

Query: 135 AGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLREQGMTIFLVE 194
              +SGGE+Q   I RA++  P+LL+LDEP+  L    I+     +E +R  G+++    
Sbjct: 154 YDRLSGGEKQRALIARAIVQQPQLLILDEPTNHLD---IRYQIQILELVRSLGISVIASI 210

Query: 195 QNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAY 234
            + N A  L D   +L+ G V    T   +L  E +   +
Sbjct: 211 HDLNLACALCDHLLLLDKGQVSAMGTPAQVLTEERIAEVF 250


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: 8
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: 326
Length adjustment: 25
Effective length of query: 212
Effective length of database: 301
Effective search space:    63812
Effective search space used:    63812
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.

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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