GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Sinorhizobium meliloti 1021

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate SMa0492 SMa0492 ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_09910
         (229 letters)



>FitnessBrowser__Smeli:SMa0492
          Length = 227

 Score =  201 bits (510), Expect = 1e-56
 Identities = 93/221 (42%), Positives = 149/221 (67%)

Query: 1   MNWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFF 60
           MN  ++   +P++  G  +T +L+ +++  G ++A+ L + R S  W +      Y + F
Sbjct: 1   MNIGIVFDAIPRMLGGIVMTFQLLLLSLAIGTMIAVLLLLMRISGRWWLSWPAQFYTYVF 60

Query: 61  RGTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQA 120
           RGTP+LVQ+F+VYYGL QF+ +R S  WP LRDPF CA + ++L+T AY++EI RG + A
Sbjct: 61  RGTPILVQIFIVYYGLPQFEWIRESIFWPILRDPFGCAILALSLNTGAYLSEIFRGGVLA 120

Query: 121 IPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTG 180
           + +G +EA  ALGMS      YI  P A RI LPAY NEVI ++K++ALAST+TL+++TG
Sbjct: 121 VERGLLEAGAALGMSATHRFIYITTPLAIRIALPAYGNEVISLMKSTALASTITLVDMTG 180

Query: 181 MARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLERWL 221
           + RTI+A T+ P ++F +  + Y+ +++++ +  K+LE +L
Sbjct: 181 IGRTIVAETFAPYQVFLSLAIVYVAITWIIQRSVKRLEVYL 221


Lambda     K      H
   0.331    0.141    0.434 

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: 156
Number of extensions: 2
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: 229
Length of database: 227
Length adjustment: 23
Effective length of query: 206
Effective length of database: 204
Effective search space:    42024
Effective search space used:    42024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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