GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS24000 in Paraburkholderia bryophila 376MFSha3.1

Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_00224 H281DRAFT_00224 amino acid ABC transporter substrate-binding protein, PAAT family

Query= uniprot:B2TBJ6
         (286 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00224 H281DRAFT_00224 amino
           acid ABC transporter substrate-binding protein, PAAT
           family
          Length = 258

 Score =  134 bits (338), Expect = 2e-36
 Identities = 85/276 (30%), Positives = 138/276 (50%), Gaps = 28/276 (10%)

Query: 15  AVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQC 74
           A+  A A+ A  A AK+WKTV I ++  Y P+      G++ GF+ +L   LC R+ ++C
Sbjct: 5   ALCVALAVMATGAMAKEWKTVRIGVDASYPPFESKAASGQVVGFDVDLTKALCARMNVKC 64

Query: 75  NLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFS-KPYAATPATFAVADAKVLPK 133
             V QD+DG+IP L+  KFD ++ ++++T +R + I FS K + A     A A + +LP 
Sbjct: 65  VWVEQDFDGIIPALKGKKFDAIVSSLTVTDKRREQIDFSDKLFDAPARMIAKAGSPLLPT 124

Query: 134 AAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDI-ATIRVYK 192
           A                        + LKGK IG++ GT    +    ++    T+  Y+
Sbjct: 125 A------------------------ESLKGKRIGVEQGTTQEAYAKAYWEPKGVTVVPYQ 160

Query: 193 TSPERDLDLANGRIDASF-DDVTYYAANIDKKETASIVMAGPKIGGP-IWGPGEGLAFRK 250
              +   DL +GR+DA+  D++   A  +          AGP++  P   G G  +  RK
Sbjct: 161 NQDQVYADLTSGRLDAALQDEIQADAGFLKTPRGKGFAWAGPEVKDPKTIGEGTAIGLRK 220

Query: 251 QDADLKAKFDTAISAALADGTVKKLSNKWFKTDVTP 286
           +DADL+  F+ A++    DGT  KL  ++F  D+ P
Sbjct: 221 EDADLRTMFNRALAQVHQDGTFTKLEKQYFDFDIYP 256


Lambda     K      H
   0.316    0.134    0.396 

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: 204
Number of extensions: 16
Number of successful extensions: 4
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: 286
Length of database: 258
Length adjustment: 25
Effective length of query: 261
Effective length of database: 233
Effective search space:    60813
Effective search space used:    60813
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: 47 (22.7 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