GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_06096
          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 (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