GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Burkholderia phytofirmans PsJN

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS15610 BPHYT_RS15610 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15610 BPHYT_RS15610
           branched-chain amino acid ABC transporter
           substrate-binding protein
          Length = 399

 Score =  363 bits (932), Expect = e-105
 Identities = 179/365 (49%), Positives = 245/365 (67%), Gaps = 3/365 (0%)

Query: 11  AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70
           A+ A  A   +++  VVKIGH AP++G  AH GKDNENGAR+AI+E+N QG+TI G KI+
Sbjct: 33  ASAATVAAAPASEATVVKIGHAAPLTGPIAHLGKDNENGARLAIDEINTQGLTIDGHKIQ 92

Query: 71  FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130
            EL A+DDAADPK GTA A+K  D  V  VVGHLNSG +IPASK+Y+D GI  ++ ++TN
Sbjct: 93  LELDAQDDAADPKTGTAVAEKFVDDHVVAVVGHLNSGVSIPASKIYSDAGILEISPSSTN 152

Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190
           P  T+ G+KTT+R++A D   G  LA YA   L  K +AI+DD + YG+G+AD F KT  
Sbjct: 153 PGYTQQGFKTTYRVVATDAQQGPALANYATKVLNAKRIAIVDDSSVYGKGLADEFAKTVQ 212

Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250
           A G K+V  + T D+AT+F A+L  IK   PD I +GGMD  GGP  +Q   LG+   K 
Sbjct: 213 ASGAKIVARESTNDRATEFQAVLRKIKRVQPDVIMFGGMDATGGPFTKQAAALGI-RAKI 271

Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310
            GGDG+CT ++ +LA  A  + N++C+E G +L+KM  G  ++ KY  ++    Q+Y+P+
Sbjct: 272 LGGDGVCTDKVGELAGTA--VQNLVCSEAGLALSKMDKGADFEKKYVDRFHTPVQIYAPF 329

Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370
           TYDA ++IVDAMKRANS++       +  + + GV   IAF+  G++K  AITLY +KDG
Sbjct: 330 TYDAVYVIVDAMKRANSIEAPKVLAAMPSTDYNGVIGHIAFDDKGDLKEGAITLYDFKDG 389

Query: 371 KKTPL 375
           KK  L
Sbjct: 390 KKAVL 394


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: 445
Number of extensions: 14
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: 399
Length adjustment: 30
Effective length of query: 345
Effective length of database: 369
Effective search space:   127305
Effective search space used:   127305
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, 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