Aligments for a candidate for nagF in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagF in Pseudomonas fluorescens FW300-N1B4

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate Pf1N1B4_1146 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1146
          Length = 953

 Score =  455 bits (1170), Expect = e-132
 Identities = 285/672 (42%), Positives = 393/672 (58%), Gaps = 16/672 (2%)

Query: 181 QVTLVHAGGLHARPAARAREAARGFDARVEVRY-EGRKAAI--ESVVGLLGLGAGEGATV 237
           ++ L +  GLHARPA    + A+ F+  + VR  +G  +A+  +S+  LL LGA  G  +
Sbjct: 286 RIALANTHGLHARPAKILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVL 345

Query: 238 ELLGMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAP---NTLA 294
           E +     AA A+ A+   +      EVE  PA   S   + +A  A   LAP   + + 
Sbjct: 346 EFIAEPTIAADALPALLAAIEEGLGEEVEPLPA--VSQHREVIADVAEVLLAPASGSLIQ 403

Query: 295 GVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRG 354
            + AAPG+A+G         ID P +   ++A E   L +A+A V  D++  + + S+  
Sbjct: 404 AIAAAPGIAIGPAHIQVQQVIDYPLRGE-SAAIERERLKQALADVRRDIEGLI-ERSKAK 461

Query: 355 AVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAER 414
           A+ E  IF  H+ +L+DP L D     +  G+SA  AW   I A      +++DALLAER
Sbjct: 462 AIRE--IFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAER 519

Query: 415 AADLRDIEKRVLRALGYTSATARTLPEEA-VLAAEEFTPSDLSTLDRSRVTALVMARGGA 473
           AADLRDI +RVL  L      A   PE+  +L  +E  PSD++ LD +RV  ++ ARGGA
Sbjct: 520 AADLRDIGRRVLAQLSGVETPAE--PEQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 577

Query: 474 TSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRL 533
           T+H+AI+AR  GIPALV  G A+  +  GT ++++   GRL        ++RA  ER   
Sbjct: 578 TAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTR 637

Query: 534 ADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAA 593
               +A      Q A+T+DG A+EV ANI       +AVE GA+ +GLLRTEL+F+  + 
Sbjct: 638 ELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQ 697

Query: 594 APTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVR 653
           AP        Y+ ++D L+GR  ++RTLDVG DK + Y  +  E NP LG+RGIRL   R
Sbjct: 698 APDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQR 757

Query: 654 PDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIE 713
           P +++ QLR LL       +RI+ PMV  V E  + R   +    E+   + +++G+MIE
Sbjct: 758 PQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVAD-LQLGIMIE 816

Query: 714 VPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQG 773
           VPSAALLA  LA+  DF S+GTNDLTQYTLA+DR    L+AQADGLHPAVL+LI  TV+ 
Sbjct: 817 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 876

Query: 774 ADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQD 833
           A  HGKWVGVCG LA DPLA+P+LVGLGV ELSV   S+  +KAR+R L     +  AQ 
Sbjct: 877 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQ 936

Query: 834 ALALESAQAVRA 845
           ALA+ SA  VRA
Sbjct: 937 ALAVGSANEVRA 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: 1736
Number of extensions: 82
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, 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