GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Azospirillum brasilense Sp245

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 AZOBR_RS27070 AZOBR_RS27070 ABC transporter permease

Query= TCDB::Q9HU29
         (230 letters)



>FitnessBrowser__azobra:AZOBR_RS27070
          Length = 220

 Score =  115 bits (287), Expect = 9e-31
 Identities = 67/215 (31%), Positives = 117/215 (54%), Gaps = 10/215 (4%)

Query: 9   KWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPLLL 68
           +W+   L G  +T+ L A  VV GL L L  G+A+ SR   +R + +AYI  FR TPLL+
Sbjct: 13  RWL--FLNGTLVTIGLTAAVVVLGLLLGLVGGLAQLSRFAVLRWISWAYIELFRCTPLLV 70

Query: 69  QLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVGEVE 128
           QL   YY L     ++         D    ++LT++L+  ++ AE++RG + S+  G+ E
Sbjct: 71  QLLWFYYALPMLTGIQI--------DAVTASVLTLSLYGGSFYAEVIRGGVVSIEAGQTE 122

Query: 129 AARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMARTIIA 188
           A  ALGM+  + +  I+LP+AV+  +P   N+ I+  K +++V  V + D++   +    
Sbjct: 123 AGLALGMTPAKVMRRIVLPQAVKRMIPPLMNQSIIQFKNTSLVSVVAVPDLLYQGQVAAT 182

Query: 189 RTYESMLFFCLAGALYLVITIVLTRIFRLIERWLR 223
            T+  +  + +   +Y V+ + LT I +  E+ L+
Sbjct: 183 DTFRPLEVYTIVALIYFVVLVPLTAIVKRGEKQLQ 217


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: 120
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 230
Length of database: 220
Length adjustment: 22
Effective length of query: 208
Effective length of database: 198
Effective search space:    41184
Effective search space used:    41184
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