GapMind for catabolism of small carbon sources

 

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

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate H281DRAFT_02563 H281DRAFT_02563 amino acid ABC transporter membrane protein, PAAT family

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__Burk376:H281DRAFT_02563
          Length = 265

 Score =  132 bits (333), Expect = 5e-36
 Identities = 83/223 (37%), Positives = 129/223 (57%), Gaps = 9/223 (4%)

Query: 5   DWSSIVPSLPYLLD-GLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVF 63
           DW  +V SLP L+  GLV TL ++V +  +GI+ G  LA+  +S    + W  + +V+VF
Sbjct: 10  DWPLLVESLPTLIGTGLVNTLILSVVSTALGIVAGMALALCAVSHTRWLTWPVRVFVDVF 69

Query: 64  RSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSI 123
           R +P  +V+L   ++  G     L L   N   L  A+VA ++  +AY +EI R+GIQS+
Sbjct: 70  RGLPAALVIL---VVGQGLAPVGLSLFGPNPYPL--AIVALALVSSAYIAEIFRSGIQSV 124

Query: 124 SRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRT 183
            RGQ SA  ALGMT+W  M+ +I+PQ  R ++P L  Q I + +D+SLVY L L    R 
Sbjct: 125 GRGQMSACQALGMTYWSGMRHVIVPQGVRRILPALANQFISIVKDSSLVYFLGLLTSQRD 184

Query: 184 ASTIGER---DGTQVEMILFAGFVYFVISLSASLLVSYLKRRT 223
             TIG+    +   +  ++ AG VY +I++  +  +++L R T
Sbjct: 185 LFTIGQNAAVNTANLSPLVAAGAVYLLITVPLTHTINHLDRWT 227


Lambda     K      H
   0.330    0.140    0.412 

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: 167
Number of extensions: 12
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: 224
Length of database: 265
Length adjustment: 24
Effective length of query: 200
Effective length of database: 241
Effective search space:    48200
Effective search space used:    48200
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 (21.9 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