GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_01194
          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 (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