Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N2E2

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate Pf6N2E2_3339 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3339
          Length = 954

 Score =  456 bits (1174), Expect = e-132
 Identities = 278/673 (41%), Positives = 386/673 (57%), Gaps = 30/673 (4%)

Query: 175 QVRIAHRGGLHARPAALVRQTAQGFKSRSQLHF---SGKSASCDSVMGMMGLAITEQAQV 231
           ++ +A+  GLHARPA ++ Q A+ F+   ++        + S  S+  ++ L       +
Sbjct: 286 RIGLANAHGLHARPAKILAQLAKSFEGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVL 345

Query: 232 HVSCRGSDAEAALQALLTTLSTALVEEAHASAPPPEPPRANA-----------EEG-VLH 279
                 S A  AL ALL  +   L EE     PPP  PR              E G ++ 
Sbjct: 346 EFIAEPSIANDALPALLAAIEEGLGEEVEP-LPPPSAPRETVMAEVATVMLAPESGSLIQ 404

Query: 280 GVCAAPGLVTGP--LVRLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARAR 337
            V AAPG+  GP  +  L  I  P  + G +   +R+RL +AL QVR +I   +E A+A+
Sbjct: 405 AVAAAPGIAIGPAHIQVLQAIDYP--LRGESAAIERERLQNALNQVRRDIQGLIERAKAK 462

Query: 338 QHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAE 397
             R+   IF  H  +L+DP L D  D  ++ G +A  AW   ++   +  + L   LLAE
Sbjct: 463 AIRE---IFITHQEMLDDPELSDEVDTRLKLGESAQAAWMGVVEAAAKEQEALQDALLAE 519

Query: 398 RANDLRDLRQRVLRVLLGEAWQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGAT 457
           RA DLRD+ +RVL  L G     +     I+   E+ PSD+ +L    VAG+    GGAT
Sbjct: 520 RAADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGAT 579

Query: 458 SHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTP---TVERLAQVRQAQT 514
           +H AI+AR  G+P LV  G  +L    G +++LD   GRL + P   T++R  + R  + 
Sbjct: 580 AHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTRE 639

Query: 515 RRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDR 574
           +R  + A+Q+   H PA T DG  VEV AN+  SA    ++  GA+G+GLLRTE +F+  
Sbjct: 640 QRLKVAAEQR---HEPALTRDGHAVEVFANIGESAGVAGAVEQGAEGIGLLRTELIFMAH 696

Query: 575 HTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQ 634
             APDE  Q   Y+ VL+ +  +P+++RT+DVGGDK L Y P+  E NP LG+RGIRL  
Sbjct: 697 SQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTL 756

Query: 635 VRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDELLHIRKRLDALGSELGLSERPQLGVM 694
            RP +++ QLRALL++      RI+ PMV  VDE    R   + L  E+ +++  QLG+M
Sbjct: 757 QRPQVMEAQLRALLRSADNRPLRIMFPMVGSVDEWRQARAMTERLRQEIPVADL-QLGIM 815

Query: 695 VEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC 754
           +EVP+AALLA  LA+  DF S+GTNDL+QYTLA+DR H  L+A+ D LHPA+L+LI  T 
Sbjct: 816 IEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITV 875

Query: 755 AGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLS 814
             A  HG+WVGVCG LA+DPLA PVL+GLGV ELSVS   I E+K RVR L  AQ   L+
Sbjct: 876 RAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLA 935

Query: 815 NELLNLGSALAVR 827
            E L +GSA  VR
Sbjct: 936 QEALAVGSADDVR 948


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: 1649
Number of extensions: 102
Number of successful extensions: 6
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: 954
Length adjustment: 43
Effective length of query: 794
Effective length of database: 911
Effective search space:   723334
Effective search space used:   723334
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.

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