Alignments for a candidate for nagF in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas fluorescens GW456-L13

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate PfGW456L13_5075 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5075
          Length = 953

 Score =  448 bits (1153), Expect = e-130
 Identities = 288/702 (41%), Positives = 393/702 (55%), Gaps = 23/702 (3%)

Query: 159 DGAAAEASRQLSSTNVTEEARQQV---------TLVHAGGLHARPAARAREAARGFDARV 209
           +G   E  R  SS  V E    +V          L +A GLHARPA    + A+ F+  +
Sbjct: 255 EGRGHELGRATSSRKVLEVLGGEVPADWPSARIALANAHGLHARPAKILAQLAKSFEGDI 314

Query: 210 EVRY-EGRKAAI--ESVVGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAHGEVE 266
            VR  +G  +A+  +S+  LL LGA  G  +E++     AA A+ A+   +      EVE
Sbjct: 315 RVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEIIAEPGIAADALPALLAAIEEGLGEEVE 374

Query: 267 EKPARQSSPAPQAVARPAGETLAPNT---LAGVCAAPGVAVGKLVRWDDADIDPPEKANG 323
             P    S A + VA  A   LAP++   +  + AAPG A+G         ID P +   
Sbjct: 375 PLPP--VSQAREVVADMAEVVLAPSSGSVVQAIAAAPGFAIGPAHIQVLQTIDYPLRGES 432

Query: 324 TSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLIS 383
                 RL   A+A V  D+   + + S+  A+ E  IF  H+ +L+DP L D     + 
Sbjct: 433 AGIERERL-QHALAQVRRDIQGLI-ERSKSKAIRE--IFITHQEMLDDPELTDEVDTRLK 488

Query: 384 LGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEA 443
            G+SA  AW   I A       ++DALLAERAADLRDI +RVL  L      +    +  
Sbjct: 489 QGESAEAAWMAVIEAAARQQETLQDALLAERAADLRDIGRRVLMQLSGIETPSEP-DQPY 547

Query: 444 VLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGT 503
           +L  +E  PSD++ LD +RV  ++ ARGGAT+H+AI+AR  GIPALV  G  +  +  GT
Sbjct: 548 ILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPGVLLLAPGT 607

Query: 504 QVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIA 563
            ++++   GRL        ++RA  ER       +A      Q A+T DG A+EV ANI 
Sbjct: 608 ALLLDGQRGRLHVDADAATLQRATAERDTREQRLKAAAELRHQPALTIDGHAVEVFANIG 667

Query: 564 TLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDV 623
                 +AVE GA+ +GLLRTEL+F+     P        Y+ ++D L+GR  ++RTLDV
Sbjct: 668 ESAGVTSAVEQGAEGIGLLRTELIFMAHPQVPDEATQEVEYRRVLDGLAGRPLVVRTLDV 727

Query: 624 GADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDV 683
           G DK + Y  +  E NP LG+RGIRL   RP +++ QLR LL       +RI+ PMV  V
Sbjct: 728 GGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSV 787

Query: 684 GELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTL 743
            E  + R   +   +E+   + +++G+MIEVPSAALLA  LA+  DF S+GTNDLTQYTL
Sbjct: 788 DEWRQARDMTERLRQEIPVAD-LQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTL 846

Query: 744 AMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVT 803
           A+DR    L+AQADGLHPAVL+LI  TV+ A  HGKWVGVCG LA DPLA+P+LVGLGV 
Sbjct: 847 AIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVD 906

Query: 804 ELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRA 845
           ELSV   S+  +KAR+R L +   +  A+ ALA+ SA  VRA
Sbjct: 907 ELSVGARSIAEVKARIRELGFTQTQTLARQALAVGSANEVRA 948


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: 1745
Number of extensions: 92
Number of successful extensions: 3
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: 953
Length adjustment: 43
Effective length of query: 811
Effective length of database: 910
Effective search space:   738010
Effective search space used:   738010
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