Alignments for a candidate for nagF in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas simiae WCS417

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate GFF780 PS417_03965 PTS fructose transporter subunit IIA

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



>FitnessBrowser__WCS417:GFF780
          Length = 952

 Score =  451 bits (1159), Expect = e-130
 Identities = 287/699 (41%), Positives = 389/699 (55%), Gaps = 18/699 (2%)

Query: 159 DGAAAEASRQLSSTNVTEEA---------RQQVTLVHAGGLHARPAARAREAARGFDARV 209
           +G   E  R  SS  V E             ++TL +A GLHARPA    + A+ FD  +
Sbjct: 255 EGRGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPAKILAQLAKSFDGDL 314

Query: 210 EVRY-EGRKAAI--ESVVGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAHGEVE 266
            VR  +G   A+  +S+  LL LGA  G  +E +     A  A+ A+   +      +VE
Sbjct: 315 RVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPALLAAVEEGLGEDVE 374

Query: 267 EKPARQSSPAPQAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSA 326
             P     P    +       LA + +  + AAPG+A+G          D P +   + A
Sbjct: 375 PLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVLQVFDYPLRGE-SCA 433

Query: 327 AESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGK 386
            E   L  A+A V  D+   + + SQ  A+ E  IF  H+ +L+DP L D     +  G+
Sbjct: 434 IERERLHSALADVRRDIQGLI-ERSQSKAIRE--IFVTHQEMLDDPELTDEVDTRLKQGE 490

Query: 387 SAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLA 446
           SA  AW   I A      +++DALLAERAADLRDI +RVL  L     T++   E  +L 
Sbjct: 491 SAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVE-TSQEPSEPYILV 549

Query: 447 AEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVV 506
            +E  PSD++ LD +RV  ++ ARGGAT+H+AI+AR  GIPALV  G A+  +  GT ++
Sbjct: 550 MDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVLLLAAGTPLL 609

Query: 507 VNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLD 566
           ++   GRL        ++RA +ER       +A      + A+T DG A+EV ANI    
Sbjct: 610 LDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVEVFANIGESA 669

Query: 567 DAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGAD 626
              +AVE GA+ +GLLRTEL+F+    AP        Y+ ++D L+GR  ++RTLDVG D
Sbjct: 670 GVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGD 729

Query: 627 KEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGEL 686
           K + Y  +  E NP LG+RGIRL   RP +++ QLR LL       +RI+ PMV  V E 
Sbjct: 730 KPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMFPMVGSVDEW 789

Query: 687 IRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMD 746
              R   +    E+   + +++G+MIEVPSAALLA  LA+  DF S+GTNDLTQYTLA+D
Sbjct: 790 RAARDMTERLRLEIPVAD-LQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAID 848

Query: 747 RCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELS 806
           R    L+AQADGLHPAVL+LI  TV+ A  HGKWVGVCG LA DPLA+P+LVGLGV ELS
Sbjct: 849 RGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELS 908

Query: 807 VDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRA 845
           V   S+P +KARVR       +  AQ ALA+ S   VRA
Sbjct: 909 VSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRA 947


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: 1732
Number of extensions: 85
Number of successful extensions: 4
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: 952
Length adjustment: 43
Effective length of query: 811
Effective length of database: 909
Effective search space:   737199
Effective search space used:   737199
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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Protein sequences (fasta format)
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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