GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Sinorhizobium meliloti 1021

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate SMa0492 SMa0492 ABC transporter permease

Query= TCDB::Q9HU29
         (230 letters)



>FitnessBrowser__Smeli:SMa0492
          Length = 227

 Score =  188 bits (478), Expect = 6e-53
 Identities = 92/217 (42%), Positives = 141/217 (64%)

Query: 6   LILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTP 65
           ++   +P+ML G  +T +LL +++  G  +A+ L + R S  W++      Y + FRGTP
Sbjct: 5   IVFDAIPRMLGGIVMTFQLLLLSLAIGTMIAVLLLLMRISGRWWLSWPAQFYTYVFRGTP 64

Query: 66  LLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVG 125
           +L+Q+FIVYYGL QFE +R+S FWP LRDP+ CA+L ++L+T AY++EI RG + +V  G
Sbjct: 65  ILVQIFIVYYGLPQFEWIRESIFWPILRDPFGCAILALSLNTGAYLSEIFRGGVLAVERG 124

Query: 126 EVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMART 185
            +EA  ALGMS      +I  P A+RI LPAY NEVI ++K++A+  T+TL D+ G+ RT
Sbjct: 125 LLEAGAALGMSATHRFIYITTPLAIRIALPAYGNEVISLMKSTALASTITLVDMTGIGRT 184

Query: 186 IIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWL 222
           I+A T+     F     +Y+ IT ++ R  + +E +L
Sbjct: 185 IVAETFAPYQVFLSLAIVYVAITWIIQRSVKRLEVYL 221


Lambda     K      H
   0.332    0.142    0.443 

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: 4
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: 230
Length of database: 227
Length adjustment: 23
Effective length of query: 207
Effective length of database: 204
Effective search space:    42228
Effective search space used:    42228
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 (22.0 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