GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Sinorhizobium meliloti 1021

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate SM_b20784 SM_b20784 branched-chain amino acid ABC transporter ATP-binding protein

Query= CharProtDB::CH_003736
         (237 letters)



>FitnessBrowser__Smeli:SM_b20784
          Length = 238

 Score =  163 bits (412), Expect = 3e-45
 Identities = 95/237 (40%), Positives = 130/237 (54%), Gaps = 5/237 (2%)

Query: 1   MEKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSG 60
           M    L  D +SA YG  + L  +S  +  G  + ++G NG GKTTLL TL G  R   G
Sbjct: 1   MPAAPLEVDNLSAGYGPTRVLEGISFSVPAGARLAVLGRNGMGKTTLLATLAGQTRRYEG 60

Query: 61  RIVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWV 120
           RI   D ++T   +A    + +  VP+ R VF  +TVEENL    F   + + +  +   
Sbjct: 61  RIRIGDANVTALPSASRALKGLGFVPQARCVFPSLTVEENL----FVGLKGRPKTALSEA 116

Query: 121 YELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTI 180
           YE+FPRL+ERR      +SGGEQQML+  R+++  P +LLLDEP  GLAP+I +++    
Sbjct: 117 YEMFPRLYERRRNLGSQLSGGEQQMLSTARSILGRPSVLLLDEPLEGLAPVICEELMKAF 176

Query: 181 EQL-REQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236
            +L +  GMTI LVEQ    AL  ADR  +LE G +  S T +AL    A     LG
Sbjct: 177 AELAKTGGMTILLVEQRIQSALDFADRVIILERGRLAWSGTPEALAKEHATVERLLG 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: 157
Number of extensions: 7
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: 237
Length of database: 238
Length adjustment: 23
Effective length of query: 214
Effective length of database: 215
Effective search space:    46010
Effective search space used:    46010
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