Alignments for a candidate for nagF in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Burkholderia phytofirmans PsJN

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate BPHYT_RS02740 BPHYT_RS02740 PTS glucose transporter subunit IIA

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>FitnessBrowser__BFirm:BPHYT_RS02740
          Length = 854

 Score = 1631 bits (4224), Expect = 0.0
 Identities = 854/854 (100%), Positives = 854/854 (100%)

Query: 1   MSHSEGHIVLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCDATVTHLAR 60
           MSHSEGHIVLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCDATVTHLAR
Sbjct: 1   MSHSEGHIVLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCDATVTHLAR 60

Query: 61  TGHAVTLATAEGAEILLHIGIDTVELNGKGFAPMVAQGAHVRAGDVLIEFDQDQVALNAP 120
           TGHAVTLATAEGAEILLHIGIDTVELNGKGFAPMVAQGAHVRAGDVLIEFDQDQVALNAP
Sbjct: 61  TGHAVTLATAEGAEILLHIGIDTVELNGKGFAPMVAQGAHVRAGDVLIEFDQDQVALNAP 120

Query: 121 SLVSVIAIANSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQ 180
           SLVSVIAIANSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQ
Sbjct: 121 SLVSVIAIANSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQ 180

Query: 181 QVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGEGATVELL 240
           QVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGEGATVELL
Sbjct: 181 QVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGEGATVELL 240

Query: 241 GMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLAGVCAAP 300
           GMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLAGVCAAP
Sbjct: 241 GMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLAGVCAAP 300

Query: 301 GVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAG 360
           GVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAG
Sbjct: 301 GVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAG 360

Query: 361 IFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRD 420
           IFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRD
Sbjct: 361 IFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRD 420

Query: 421 IEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAIL 480
           IEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAIL
Sbjct: 421 IEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAIL 480

Query: 481 ARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREAN 540
           ARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREAN
Sbjct: 481 ARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREAN 540

Query: 541 RRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEH 600
           RRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEH
Sbjct: 541 RRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEH 600

Query: 601 RQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQ 660
           RQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQ
Sbjct: 601 RQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQ 660

Query: 661 LRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALL 720
           LRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALL
Sbjct: 661 LRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALL 720

Query: 721 ADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKW 780
           ADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKW
Sbjct: 721 ADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKW 780

Query: 781 VGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESA 840
           VGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESA
Sbjct: 781 VGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESA 840

Query: 841 QAVRAASRETWPLD 854
           QAVRAASRETWPLD
Sbjct: 841 QAVRAASRETWPLD 854


Lambda     K      H
   0.317    0.133    0.371 

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: 2239
Number of extensions: 59
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: 854
Length of database: 854
Length adjustment: 42
Effective length of query: 812
Effective length of database: 812
Effective search space:   659344
Effective search space used:   659344
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources