GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Klebsiella michiganensis M5al

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate BWI76_RS26330 BWI76_RS26330 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003736
         (237 letters)



>FitnessBrowser__Koxy:BWI76_RS26330
          Length = 233

 Score =  442 bits (1136), Expect = e-129
 Identities = 223/233 (95%), Positives = 227/233 (97%)

Query: 5   MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64
           MLSFD VSAHYGKIQALH VSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRA+SGR+VF
Sbjct: 1   MLSFDNVSAHYGKIQALHNVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRASSGRVVF 60

Query: 65  DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYELF 124
           D KDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFA+RDQFQ RIKWVYELF
Sbjct: 61  DGKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFADRDQFQTRIKWVYELF 120

Query: 125 PRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLR 184
           PRLHERR+QRAGTMSGGEQQMLAIGRALMS PRLLLLDEPSLGLAPIIIQQIFDTIEQLR
Sbjct: 121 PRLHERRVQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPIIIQQIFDTIEQLR 180

Query: 185 EQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLGG 237
           EQGMTIFLVEQNANQALKLADRGYVLENGHVVL DTGDALLANEAVRSAYLGG
Sbjct: 181 EQGMTIFLVEQNANQALKLADRGYVLENGHVVLEDTGDALLANEAVRSAYLGG 233


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: 318
Number of extensions: 11
Number of successful extensions: 1
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: 233
Length adjustment: 23
Effective length of query: 214
Effective length of database: 210
Effective search space:    44940
Effective search space used:    44940
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: 46 (22.3 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