GapMind for catabolism of small carbon sources

 

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

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate H281DRAFT_06096 H281DRAFT_06096 amino acid/amide ABC transporter substrate-binding protein, HAAT family

Query= SwissProt::P21175
         (373 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06096 H281DRAFT_06096 amino
           acid/amide ABC transporter substrate-binding protein,
           HAAT family
          Length = 383

 Score =  201 bits (512), Expect = 2e-56
 Identities = 117/357 (32%), Positives = 190/357 (53%), Gaps = 6/357 (1%)

Query: 12  FAAMAIAGFASYSMAAD--TIKIALAGPVTGPVAQYGDMQRAGALMAIEQIN-KAGGVNG 68
           FA   +     ++ AAD   +KI   GP+TGPVA+ G   + GA +AI++ N +   V G
Sbjct: 10  FAVCLLGAQTPFASAADPEVVKIGFVGPLTGPVARVGKDLQYGAQLAIDEENARHPTVGG 69

Query: 69  AQLEGV--IYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITP 126
             ++ V  + DD  DP+ A+ VA K+V+DGV  V+GH  S  + PA+ +Y    V MITP
Sbjct: 70  KPVKFVLDVQDDQADPRVAIQVAQKLVDDGVVGVIGHYNSGCSIPASTVYHQANVAMITP 129

Query: 127 SATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVK 186
            +T P++T +GYK +FRT+G D + G VAG F+ E+ K K I ++ D+  +G+G+A   +
Sbjct: 130 GSTNPQLTKQGYKNVFRTMGHDGIGGVVAGHFVVEQMKAKRIGIIDDRTAFGQGLADAFE 189

Query: 187 KTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLD 246
           K  ++A   + V E  N    DF A+++ LK   V  ++FGG   +  +L++Q +  G++
Sbjct: 190 KGAKEANGNIVVREFTNDKAVDFRAILTTLKSRNVDLIFFGGLDEQGAMLIKQMRSLGMN 249

Query: 247 ARFMGPEGVGNSEITAIAGDASEGMLATLP-RAFEQDPKNKALIDAFKAKNQDPSGIFVL 305
           A+  G   + ++    IAG A +G     P  A ++ P        +KA+      ++  
Sbjct: 250 AQLFGAGALKSNAFLQIAGTAGDGTQDLEPGPALDKQPAALEFGKRYKARFNQDVELYAP 309

Query: 306 PAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYE 362
            AY A   + K I  A   D  K+ ++L        TG + FD  GDL    +T+++
Sbjct: 310 FAYDAALAMLKAIHTANSLDRSKIVDSLSKVNVTGVTGQIAFDPYGDLIKPPYTLFQ 366


Lambda     K      H
   0.316    0.133    0.377 

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: 345
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: 373
Length of database: 383
Length adjustment: 30
Effective length of query: 343
Effective length of database: 353
Effective search space:   121079
Effective search space used:   121079
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: 41 (21.6 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