GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01115 in Burkholderia phytofirmans PsJN

Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate BPHYT_RS25800 BPHYT_RS25800 sugar ABC transporter permease

Query= reanno::Burk376:H281DRAFT_01115
         (357 letters)



>FitnessBrowser__BFirm:BPHYT_RS25800
          Length = 352

 Score =  639 bits (1649), Expect = 0.0
 Identities = 322/348 (92%), Positives = 334/348 (95%)

Query: 1   MKSSFAAGKLFADRQLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALG 60
           MKS+F AGKLF DRQLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALG
Sbjct: 1   MKSAFTAGKLFGDRQLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALG 60

Query: 61  IMLSMVSGNGGIDLSGVGLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGG 120
           IMLSMVSGNGGIDLSGVGLANLSGMVAA++VPR VNGDDSP LYTSLFC IV+ MGLLGG
Sbjct: 61  IMLSMVSGNGGIDLSGVGLANLSGMVAALIVPRFVNGDDSPALYTSLFCVIVVTMGLLGG 120

Query: 121 LLNGVVIARLRLTPILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIA 180
           LLNGVVIARLRLTPILCTLGTQLLFTGFAVV+SNGASVHVDYV+PLS+IGNGTV QVPIA
Sbjct: 121 LLNGVVIARLRLTPILCTLGTQLLFTGFAVVLSNGASVHVDYVDPLSNIGNGTVFQVPIA 180

Query: 181 FCIFLAAVIVLGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAG 240
           FCIF+AAVIVLGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAG
Sbjct: 181 FCIFIAAVIVLGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAG 240

Query: 241 LISATHTSSAKWDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLL 300
           LIS THTSSAKWDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNL+
Sbjct: 241 LISVTHTSSAKWDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLM 300

Query: 301 GVSQFFGDCAWGFLLLLSLAFAGGERVRAIFGLGGGGGSTQPAKPPAS 348
           GVSQFFGDCAWGFLLLLSLAFAGGERVRAIFG GGG G++  A P +S
Sbjct: 301 GVSQFFGDCAWGFLLLLSLAFAGGERVRAIFGFGGGAGASNAASPASS 348


Lambda     K      H
   0.327    0.143    0.429 

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: 583
Number of extensions: 11
Number of successful extensions: 1
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: 357
Length of database: 352
Length adjustment: 29
Effective length of query: 328
Effective length of database: 323
Effective search space:   105944
Effective search space used:   105944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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