GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Acidovorax sp. GW101-3H11

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Ac3H11_1958 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1958
          Length = 245

 Score =  266 bits (679), Expect = 4e-76
 Identities = 136/242 (56%), Positives = 179/242 (73%), Gaps = 3/242 (1%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +E+ N++KWYG   VL + +  + +GE +V+ GPSGSGKST+I+ IN LE  QKG+I VD
Sbjct: 2   IELKNVSKWYGPVQVLNECSATINKGEVVVVCGPSGSGKSTLIKTINALEPFQKGEITVD 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G +L +    + ++R  VGMVFQHF LFPHL++ +N T+A I V      +A++  +  L
Sbjct: 62  GVKLHDPSTNLPKLRSRVGMVFQHFELFPHLSVTDNLTIAQIKVLGRSADEAKKRGLKML 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
           +RV +    +K+PGQLSGGQQQRVAIAR+L M+P +MLFDEPTSALDPEM+ EVLD MVG
Sbjct: 122 ERVGLIAHKDKFPGQLSGGQQQRVAIARALSMDPIVMLFDEPTSALDPEMVGEVLDVMVG 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMD-QGQIVEQNEPAAFFDNP--QHERTKLFLSQ 254
           LA EGMTM+CVTHEMGFAR+V+NRVIFMD  G+I+E      FF+NP  +  RTK FL++
Sbjct: 182 LANEGMTMMCVTHEMGFARKVSNRVIFMDVGGKILEDCSKDEFFNNPDARQPRTKDFLNK 241

Query: 255 IL 256
           IL
Sbjct: 242 IL 243


Lambda     K      H
   0.321    0.135    0.394 

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: 206
Number of extensions: 10
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: 257
Length of database: 245
Length adjustment: 24
Effective length of query: 233
Effective length of database: 221
Effective search space:    51493
Effective search space used:    51493
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 (21.9 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