GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapP in Bacteroides thetaiotaomicron VPI-5482

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 352022 BT2494 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q52815
         (257 letters)



>lcl|FitnessBrowser__Btheta:352022 BT2494 ABC transporter,
           ATP-binding protein (NCBI ptt file)
          Length = 238

 Score =  142 bits (359), Expect = 5e-39
 Identities = 82/224 (36%), Positives = 134/224 (59%), Gaps = 9/224 (4%)

Query: 18  VEIVNMNKWYGD---FHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKI 74
           +++ ++NK Y +    HVL+ INL + RGE + I G SGSGKST++  +  L+ +  G  
Sbjct: 2   IKLTDINKTYNNGAPLHVLKGINLDIQRGEFVSIMGASGSGKSTLLNILGILDNYDTGDY 61

Query: 75  VVDGTELTN--DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132
            ++   + +  + K  +   R +G +FQ FNL      +EN  L P++ + + +K+   +
Sbjct: 62  YLNNVLIKDLSETKAAEYRNRMIGFIFQSFNLISFKDAVENVAL-PLFYQGVSRKKRNAL 120

Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192
           A+ +L R+ + E A+  P ++SGGQ+QRVAIAR+L   P+I+L DEPT ALD +   EV+
Sbjct: 121 ALEYLDRLGLKEWAHHMPNEMSGGQKQRVAIARALITQPQIILADEPTGALDSKTSVEVM 180

Query: 193 DTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQI--VEQN 234
             +  L   GMT++ VTHE G A Q  +++I +  G I  +E+N
Sbjct: 181 QILKDLHRMGMTIVVVTHESGVANQ-TDKIIHIKDGIIERIEEN 223


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: 129
Number of extensions: 8
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: 238
Length adjustment: 24
Effective length of query: 233
Effective length of database: 214
Effective search space:    49862
Effective search space used:    49862
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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