Alignments for a candidate for nagF in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Stenotrophomonas chelatiphaga DSM 21508

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate WP_057508246.1 ABB28_RS08640 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HXN5
         (842 letters)



>NCBI__GCF_001431535.1:WP_057508246.1
          Length = 585

 Score =  305 bits (781), Expect = 5e-87
 Identities = 218/586 (37%), Positives = 299/586 (51%), Gaps = 28/586 (4%)

Query: 265 PRAIAPGEPA--RPAAVAGTLAGVCASPGLASGPLARLGAISLPADDGRHRPEEQ----- 317
           PRA A   P   RP  +   L+G  AS G A G      A +L   + R  P++      
Sbjct: 2   PRARAGLAPTGLRPVQL---LSGHGASRGTALGRARVRLAHALEVAEQRVAPQQVDKELK 58

Query: 318 --HLALDQALQRVRDDVQGSLQQARLGGDENEAAIF-SAHLALLEDPGLLDAADMLIDQG 374
             H+ALD A   + D     L+Q   G    EA  F   H  LL+DP LL   D LI  G
Sbjct: 59  RLHVALDAARNEMHD-----LRQRLQGALNQEAGEFLDLHALLLDDPELLFGLDELIRSG 113

Query: 375 -VGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLRVLLGDTAP-LRVPAGAI 432
              A +A         ++   + +  L  R +DL  +  R+   L     P ++  AG I
Sbjct: 114 PYSAGYALRLQRDRLAKVFDGMDDAYLKSRMDDLDHVIGRIHAFLQPVLPPAVKGLAGEI 173

Query: 433 VAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQ 492
           +    I PS++A L   G   +    G A SH AILARS  LP +V +   L ++ +G  
Sbjct: 174 LVCDNIAPSEMAQLQSQGVVAIVTTAGSALSHSAILARSLHLPLIVNVPGLLHKVSDGDV 233

Query: 493 VVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVAS 552
           +++D   G + ++P A  L    +++ +   ++R       + + TRD   I + AN  S
Sbjct: 234 LIVDGSDGSITVNPQAENLRDYRVRLKEHAREQRELGRLRSKPSRTRDQVDIALLANAES 293

Query: 553 PREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVG 612
             +  +A A GA G+GL RTEFLFL+R   PDEEEQ + Y++    M  R V IRT+D+G
Sbjct: 294 LEDVTQAHAFGAQGLGLYRTEFLFLQRNELPDEEEQFHTYRDAALGMAGRLVTIRTLDLG 353

Query: 613 GDK-HLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEV 671
            DK     L L  EENPALGLRG+ L  ARP + D QLRA+LR     + RIL+PMVS  
Sbjct: 354 ADKADRTGLTLSNEENPALGLRGVRLSLARPLVADTQLRAILRASAYGKVRILIPMVSTR 413

Query: 672 DELRAIRRRLGELATQLGI------ERLPELGVMIEVPSAALLADQLAEHADFLSIGTND 725
           +EL A+RRR+  L  QL        ER+P LG MIEVP+AA   +   +  DFLSIGTND
Sbjct: 414 EELLAVRRRMTRLTAQLRAEGHAVSERVP-LGAMIEVPAAAFALESFIDLVDFLSIGTND 472

Query: 726 LSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVL 785
           L QY LA DR +  L +    LHPA+LRL+        RH   V VCG +A D    P+L
Sbjct: 473 LVQYLLAADRNNEALGELYSPLHPAVLRLLKLVIETGQRHQIPVAVCGEIAGDARLAPLL 532

Query: 786 VGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAV 831
           + LG+ E S+ P  + E++  +R+ D  E R  A  LL     R++
Sbjct: 533 LALGLTEFSLHPGTLLEVRRAIRESDLGELRARAPKLLAARDRRSI 578


Lambda     K      H
   0.319    0.136    0.390 

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: 1111
Number of extensions: 59
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 842
Length of database: 585
Length adjustment: 39
Effective length of query: 803
Effective length of database: 546
Effective search space:   438438
Effective search space used:   438438
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 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