GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Sinorhizobium meliloti 1021

Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate SMc00138 SMc00138 amino acid ABC transporter permease

Query= uniprot:Q88GX2
         (236 letters)



>FitnessBrowser__Smeli:SMc00138
          Length = 276

 Score =  271 bits (693), Expect = 1e-77
 Identities = 133/224 (59%), Positives = 169/224 (75%)

Query: 12  DPDLLERYGPRFIDGLLVTAKLVAISFSLGAVLGLLLALARLSRSLVLQRMAAGYVYFFR 71
           DP+   RYGP F+ GL VT  LV  S  +GAVL L +AL R+S++ +   +A  YVYFFR
Sbjct: 51  DPEKFSRYGPSFLSGLGVTLTLVISSILMGAVLSLPVALGRMSKNRLWGWLAYAYVYFFR 110

Query: 72  GSPLLAQLFLLYYGLGSLKGFWQDVGLWWFFRDAWFCTLLAFTLNTAAYQAEIFRGSLMA 131
           G+PL+ QLFL+YYGLGS +   + VGLWWFFRDAW C L  FTLNTAAYQAEI RG++ +
Sbjct: 111 GTPLITQLFLIYYGLGSFRPQLETVGLWWFFRDAWNCALFTFTLNTAAYQAEILRGAIES 170

Query: 132 VAPGQHEAARALNLKRSTTFFKVILPQSLLVAIGPLGNELILMIKASAIASLVTIYDLMG 191
           V  GQ E A AL L     FFKVILPQ+++VA+ P GNE+ILMIK SAI ++VT++DLMG
Sbjct: 171 VPRGQREGAAALGLPERVAFFKVILPQAMIVALRPYGNEIILMIKGSAIVAIVTVFDLMG 230

Query: 192 VTKLAFSRSFDFQIYLWAAVLYLVIVELVRRLLKHLEARLGRHL 235
            T+ AFSR+FD+Q+Y+WAA+LYL++VEL+R +   LEARL RHL
Sbjct: 231 ETRRAFSRTFDYQMYIWAAILYLLMVELLRNIWGWLEARLTRHL 274


Lambda     K      H
   0.331    0.144    0.433 

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: 208
Number of extensions: 6
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: 236
Length of database: 276
Length adjustment: 24
Effective length of query: 212
Effective length of database: 252
Effective search space:    53424
Effective search space used:    53424
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: 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