GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate H281DRAFT_02572 H281DRAFT_02572 amino acid ABC transporter membrane protein, PAAT family

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>FitnessBrowser__Burk376:H281DRAFT_02572
          Length = 218

 Score =  117 bits (294), Expect = 1e-31
 Identities = 73/214 (34%), Positives = 117/214 (54%), Gaps = 13/214 (6%)

Query: 26  LSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWY 85
           L G   TI I   A++++ +LG +L +M+   NR +S   +  + L R +P++VQLF  Y
Sbjct: 14  LKGAVITIEITACAFVLSSVLGLVLALMKVSRNRALSTFGSTVINLIRGLPIIVQLFYIY 73

Query: 86  FLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAA 145
           F++PD+    IQ           SAF + V+ LG+  +A   E  R GI+A+  GQ  AA
Sbjct: 74  FVLPDM---GIQ----------LSAFQAGVIGLGIAYSAYQAENFRAGIEAIDHGQIEAA 120

Query: 146 RAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFS 205
            A+G + P I   V+LPQA+RI +PP  +  + + K+SSVAS I + E+    +  A  +
Sbjct: 121 HAIGMRGPLIMRRVVLPQAFRIALPPYGNTLVMLLKDSSVASTITVAEITRAGQLIASST 180

Query: 206 ANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVAV 239
                 +TL  L+Y  L++ LM  +  + K +A+
Sbjct: 181 FQNMTVYTLVALLYLALSLPLMFGVNQLGKHLAL 214


Lambda     K      H
   0.326    0.140    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: 113
Number of extensions: 4
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: 248
Length of database: 218
Length adjustment: 23
Effective length of query: 225
Effective length of database: 195
Effective search space:    43875
Effective search space used:    43875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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