GapMind for catabolism of small carbon sources

 

Alignments 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_RS01885 BPHYT_RS01885 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__BFirm:BPHYT_RS01885
          Length = 381

 Score =  397 bits (1019), Expect = e-115
 Identities = 196/375 (52%), Positives = 263/375 (70%), Gaps = 3/375 (0%)

Query: 1   MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60
           +Q  L ++  A + A    ++A + VVKIGHVAP++G  AH GKDNENGAR+A+EE+NA+
Sbjct: 5   IQKLLPISAAAMLFATLATSAAADTVVKIGHVAPLTGGIAHLGKDNENGARLAVEEINAK 64

Query: 61  GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120
           G+TIGG+KI  +L A+DDAADP+  T  AQKL D KV  VVGHLNSGT+IPASK+Y+D G
Sbjct: 65  GLTIGGQKITLQLDAQDDAADPRTATQVAQKLVDDKVVAVVGHLNSGTSIPASKIYSDAG 124

Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180
           I  ++ +ATNP  T+ G+KTT+R++A D   G  LA YA   LK+K+VAI+DD TAYGQG
Sbjct: 125 IVQISPSATNPAYTQQGFKTTYRVVATDAQQGPALANYAAKGLKVKSVAIVDDSTAYGQG 184

Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240
           +A+ F+KTA + G+ V+    T DKA DF AILT IK +NPDAI YGGMD  GGP  +Q 
Sbjct: 185 LANEFEKTAKSLGLNVMSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPFAKQA 244

Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY 300
           +QLG+   K   GDG+CT ++A LA  A    N++C+E G +L KM GG+A+ AKY  ++
Sbjct: 245 KQLGL-RAKVLAGDGVCTDKLADLAGDA--TDNIVCSEAGMALEKMAGGSAFLAKYQKRF 301

Query: 301 PNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNP 360
               Q+Y+P+TYDA ++IVDAMKRANS DP      +  + +KGV     F+  G++++ 
Sbjct: 302 GQPIQIYAPFTYDAVYIIVDAMKRANSTDPAKILAAMPSTDYKGVIGETTFDSKGDLQHG 361

Query: 361 AITLYVYKDGKKTPL 375
            I+LY YK GKKT L
Sbjct: 362 VISLYNYKSGKKTLL 376


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: 475
Number of extensions: 15
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: 381
Length adjustment: 30
Effective length of query: 345
Effective length of database: 351
Effective search space:   121095
Effective search space used:   121095
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