Aligments for a candidate for nagF in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagF in Pseudomonas fluorescens FW300-N2C3

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter

Query= reanno::pseudo5_N2C3_1:AO356_17540
         (837 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17540 AO356_17540 PTS
           N-acetyl-D-glucosamine transporter
          Length = 837

 Score = 1627 bits (4212), Expect = 0.0
 Identities = 837/837 (100%), Positives = 837/837 (100%)

Query: 1   MPNNNKELILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVAR 60
           MPNNNKELILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVAR
Sbjct: 1   MPNNNKELILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVAR 60

Query: 61  TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCK 120
           TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCK
Sbjct: 61  TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCK 120

Query: 121 SLVSLLVITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQVRIAH 180
           SLVSLLVITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQVRIAH
Sbjct: 121 SLVSLLVITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQVRIAH 180

Query: 181 RGGLHARPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDA 240
           RGGLHARPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDA
Sbjct: 181 RGGLHARPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDA 240

Query: 241 EAALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQL 300
           EAALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQL
Sbjct: 241 EAALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQL 300

Query: 301 PEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLD 360
           PEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLD
Sbjct: 301 PEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLD 360

Query: 361 AADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLGEAWQF 420
           AADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLGEAWQF
Sbjct: 361 AADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLGEAWQF 420

Query: 421 DVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELL 480
           DVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELL
Sbjct: 421 DVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELL 480

Query: 481 AQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVE 540
           AQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVE
Sbjct: 481 AQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVE 540

Query: 541 VAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVI 600
           VAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVI
Sbjct: 541 VAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVI 600

Query: 601 IRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILL 660
           IRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILL
Sbjct: 601 IRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILL 660

Query: 661 PMVTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTND 720
           PMVTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTND
Sbjct: 661 PMVTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTND 720

Query: 721 LSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVL 780
           LSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVL
Sbjct: 721 LSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVL 780

Query: 781 IGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRHWPLG 837
           IGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRHWPLG
Sbjct: 781 IGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRHWPLG 837


Lambda     K      H
   0.319    0.134    0.386 

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: 2061
Number of extensions: 75
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: 837
Length of database: 837
Length adjustment: 42
Effective length of query: 795
Effective length of database: 795
Effective search space:   632025
Effective search space used:   632025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)

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

Downloads

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

Related tools

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 preprint on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources