GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Azospirillum brasilense Sp245

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate AZOBR_RS29680 AZOBR_RS29680 ABC transporter ATP-binding protein

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__azobra:AZOBR_RS29680
          Length = 272

 Score =  224 bits (572), Expect = 1e-63
 Identities = 119/254 (46%), Positives = 161/254 (63%), Gaps = 1/254 (0%)

Query: 1   MSQPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGG 60
           ++ P+L V  + + F GL+A+ +++  +   EIVSLIGPNGAGKTT FN +TGF KPTGG
Sbjct: 13  LAGPVLEVREVAVHFSGLIAIASMSFAVPEGEIVSLIGPNGAGKTTAFNVITGFLKPTGG 72

Query: 61  TILLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKT 120
            +L R   L  L   +IA +GVVRTFQ   +F   TV +N+L   H+Q +   +  LL+ 
Sbjct: 73  KVLFRGTDLTRLSSNRIAGLGVVRTFQRTSIFAGCTVFDNVLTGMHRQGRAETWGALLRL 132

Query: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180
            S R          A  L  +GL   A+  A NLAYG+QR L IA  +   P++L+LDEP
Sbjct: 133 ASVRAETERMRAAVAEILAFVGLSHRADELAGNLAYGEQRLLGIAIALAADPKLLLLDEP 192

Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQ 240
           AAGLNP ET+    ++  +R+    TILL+EHDM++VM ISDR+ V+N G  +A G PE 
Sbjct: 193 AAGLNPSETEAFMGVVQRIRD-RGVTILLVEHDMRMVMTISDRVVVLNHGRIIAEGPPEV 251

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


Lambda     K      H
   0.320    0.137    0.395 

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: 207
Number of extensions: 13
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:

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