GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Paraburkholderia bryophila 376MFSha3.1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_01194 H281DRAFT_01194 amino acid/amide ABC transporter substrate-binding protein, HAAT family (TC 3.A.1.4.-)

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01194 H281DRAFT_01194 amino
           acid/amide ABC transporter substrate-binding protein,
           HAAT family (TC 3.A.1.4.-)
          Length = 383

 Score =  306 bits (785), Expect = 5e-88
 Identities = 165/365 (45%), Positives = 226/365 (61%), Gaps = 5/365 (1%)

Query: 12  AIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKF 71
           A+A A    +A    VKIG  AP++G QAHYG D  +G ++AIE++N     IGGK + F
Sbjct: 17  ALAGAPCSYAATPVDVKIGFAAPLTGGQAHYGADFRSGVQLAIEDMNGTNPVIGGKPVHF 76

Query: 72  ELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNP 131
            L A+DD ADP+ GT  AQKL D  V  V+GH NSGT+IPA+ +Y   G P V   AT P
Sbjct: 77  VLDAQDDQADPRTGTTVAQKLVDDGVVAVIGHYNSGTSIPAAPIYAKAGTPQVA-MATAP 135

Query: 132 NLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTATA 191
           + T+ G  TTFR++ +D  LGA L  +AV  LK K +AI+DDRTAYGQGVA+ F K A A
Sbjct: 136 SYTRLGLPTTFRLLTSDTQLGAVLGDFAVKGLKFKRLAIVDDRTAYGQGVAEEFAKAAKA 195

Query: 192 KGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYF 251
            G  VV E++T DKA DF AILT IK  N DA+FYGG D Q  PML+QM  L + +    
Sbjct: 196 AGATVVTEEYTNDKAVDFRAILTKIKQANVDAVFYGGADTQAAPMLKQMRSLAIKST-LL 254

Query: 252 GGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPYT 311
           G D + +  + K+A  A      + A  GS L++MPGG A+  +Y  ++    ++Y+PY 
Sbjct: 255 GPDMLQSDNLIKIAGEASE--GTLAASEGSPLSQMPGGKAFAERYQKRFNQPVELYAPYA 312

Query: 312 YDATFLIVDAMKRANSVDPKVYTPELAKSSFKGV-TSTIAFEPNGEMKNPAITLYVYKDG 370
           YD T  + +AMK+A+S DP V+   L  ++ KGV TS ++++  G++K   +T+Y   +G
Sbjct: 313 YDGTMAVFNAMKKADSTDPHVFLSALKATNMKGVTTSELSYDQYGDLKYGGVTVYKVVNG 372

Query: 371 KKTPL 375
              PL
Sbjct: 373 TWKPL 377


Lambda     K      H
   0.315    0.131    0.375 

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: 433
Number of extensions: 12
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: 375
Length of database: 383
Length adjustment: 30
Effective length of query: 345
Effective length of database: 353
Effective search space:   121785
Effective search space used:   121785
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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, the preprint on GapMind for carbon sources, 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