GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Burkholderia phytofirmans PsJN

Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00160 BPHYT_RS00160 ABC transporter substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_2958
         (260 letters)



>FitnessBrowser__BFirm:BPHYT_RS00160
          Length = 262

 Score =  212 bits (540), Expect = 6e-60
 Identities = 118/258 (45%), Positives = 158/258 (61%), Gaps = 4/258 (1%)

Query: 3   KALLTLSALALCMAAGVAT--AKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAIC 60
           K L  L ALA   A+  A+  A     LRFG++  Y PFESK  +G L G DID+GNA+C
Sbjct: 2   KLLKPLLALACAFASLAASSGASAADTLRFGLEAQYPPFESKGPNGELQGLDIDVGNAVC 61

Query: 61  AELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKK 120
               + CKWVE+ FDG+IP L+  KFD + S+M  T AR +AIDF++ ++  PT  + K+
Sbjct: 62  VAAHMTCKWVETSFDGLIPALQGRKFDAINSAMNATDARRQAIDFTTVVYRVPTQLIAKR 121

Query: 121 GSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAA 180
            SGL    ASLKGK VG  Q +IQE YAKA  + AGV    YQ+Q+QVY DL +GRLDA 
Sbjct: 122 DSGLLPTPASLKGKRVGVLQASIQETYAKAHWESAGVTVVPYQDQNQVYTDLVAGRLDAT 181

Query: 181 IQDMLQAELGFLKSPKGEGYE-VSKPV-DSELLPSKTAIGIRKGNSELKALLNKGIKALH 238
           +      + GFL  P GEGY  V +PV D ++L S  A GIRKG++ L+  LN  I  + 
Sbjct: 182 LVLAPAGQTGFLSKPSGEGYAFVGEPVRDDKILGSGIAYGIRKGDTALRDRLNAAIAKVQ 241

Query: 239 DDGKYAEIQKKHFGDLNL 256
            DG    +  K+ G++++
Sbjct: 242 ADGTVKTLAAKYLGNIDV 259


Lambda     K      H
   0.313    0.132    0.368 

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: 185
Number of extensions: 8
Number of successful extensions: 2
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: 260
Length of database: 262
Length adjustment: 25
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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 (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