GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Azospirillum brasilense Sp245

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate AZOBR_RS29680 AZOBR_RS29680 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS29680 AZOBR_RS29680 ABC
           transporter ATP-binding protein
          Length = 272

 Score =  222 bits (566), Expect = 5e-63
 Identities = 113/254 (44%), Positives = 161/254 (63%), Gaps = 1/254 (0%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           ++ P+LEV  + + F GL+A+  ++  V E ++VS+IGPNGAGKTT FN +TGF +PTGG
Sbjct: 13  LAGPVLEVREVAVHFSGLIAIASMSFAVPEGEIVSLIGPNGAGKTTAFNVITGFLKPTGG 72

Query: 61  LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120
            +   G ++  L  ++IA  GVVRTFQ   +F   T  +N+L   HR         L + 
Sbjct: 73  KVLFRGTDLTRLSSNRIAGLGVVRTFQRTSIFAGCTVFDNVLTGMHRQGRAETWGALLRL 132

Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180
            + R          A  L  V L+  A+  AG LAYG+QR L IA  +   P++L+LDEP
Sbjct: 133 ASVRAETERMRAAVAEILAFVGLSHRADELAGNLAYGEQRLLGIAIALAADPKLLLLDEP 192

Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240
           AAGLNP ET+    ++ ++R +  VT+LL+EHDM++VM+ISD +VV+N G  +A+G PE 
Sbjct: 193 AAGLNPSETEAFMGVVQRIR-DRGVTILLVEHDMRMVMTISDRVVVLNHGRIIAEGPPEV 251

Query: 241 IRDNPDVIKAYLGE 254
           IR NPDVI+AYLG+
Sbjct: 252 IRANPDVIQAYLGQ 265


Lambda     K      H
   0.320    0.137    0.391 

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: 176
Number of extensions: 9
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: 255
Length of database: 272
Length adjustment: 25
Effective length of query: 230
Effective length of database: 247
Effective search space:    56810
Effective search space used:    56810
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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