GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS04175 CA265_RS04175 phosphonate ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Pedo557:CA265_RS04175
          Length = 232

 Score =  141 bits (356), Expect = 1e-38
 Identities = 84/222 (37%), Positives = 128/222 (57%), Gaps = 8/222 (3%)

Query: 18  VEIVNMNKWYGDFHV----LRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK 73
           ++I N+ K Y    V    L  INL V  GE + I GPSG GKST++  +  L++ + G 
Sbjct: 2   IKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENGS 61

Query: 74  IVVDGTELT--NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEE 131
                TEL   ND ++ +  +R +G VFQ+FNL   LT+ EN  L P+   K+P  + ++
Sbjct: 62  YKFIDTELLTLNDRERSNFRKRNMGFVFQNFNLIDELTVFENIEL-PLIYNKIPAGERKK 120

Query: 132 VAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEV 191
           +    ++R+ I  ++  +P QLSGGQQQRVA+AR+L   PK++L DEPT  LD     EV
Sbjct: 121 LVNEIIERMNIVNRSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNEV 180

Query: 192 LDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQ 233
           ++ +  L E G T++ VTH    A   +NR+I +  G ++ +
Sbjct: 181 MELLCELNETGTTIVMVTHSSHDA-SFSNRIINLKDGHVISE 221


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: 151
Number of extensions: 10
Number of successful extensions: 3
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: 232
Length adjustment: 24
Effective length of query: 233
Effective length of database: 208
Effective search space:    48464
Effective search space used:    48464
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