Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N2C3

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 AO356_07335 AO356_07335 PTS fructose transporter subunit IIA

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07335
          Length = 954

 Score =  462 bits (1189), Expect = e-134
 Identities = 287/670 (42%), Positives = 383/670 (57%), Gaps = 21/670 (3%)

Query: 177 RARVAHHGGLHARPAALLRKTAQGFSSQAELHFA-GQVASVD--SLVGIMGLGVAEQDEV 233
           R  +A+  GLHARPA +L + A+ F  +  +    GQ ++V   SL  ++ LG      +
Sbjct: 286 RIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVL 345

Query: 234 EVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLA--------G 285
           E I     +  AL ALLAA+        +  P   AP E          LA         
Sbjct: 346 EFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLIQA 405

Query: 286 VCASPGLASGP--LARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGG 343
           V A+PG+A GP  +  L AI  P        E + L    AL +VR D+QG +++A+   
Sbjct: 406 VAAAPGIAIGPAHIQVLQAIDYPLRGESAAIERERL--QNALNQVRSDIQGLIERAKAKA 463

Query: 344 DENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAER 403
                 IF  H  +L+DP L D  D  +  G  A  AW   I+A  +  +AL + LLAER
Sbjct: 464 IRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAER 520

Query: 404 ANDLRDLEKRVLRVLLGDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATS 463
           A DLRD+ +RVL  L G   P       I+   E+ PSD+A L     AG+  A GGAT+
Sbjct: 521 AADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATA 580

Query: 464 HVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREE 523
           H AI+AR+ G+P LV  GA +L L  G  ++LD  +GRL + PDA  L++ A +     E
Sbjct: 581 HSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQR-AKEERDTRE 639

Query: 524 QRRRQQADAQRE-ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAA 582
           QR +  A+ + E ALTRDG  +E+ AN+      A A   GA+G+GLLRTE +F+    A
Sbjct: 640 QRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQA 699

Query: 583 PDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARP 642
           PDE  Q   Y++VLD +  R +++RT+DVGGDK L Y P+  EENP LG+RGI L   RP
Sbjct: 700 PDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRP 759

Query: 643 ELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEV 702
           ++++ QLRALLR       RI+ PMV  VDE R  R     L  ++ +  L +LG+MIEV
Sbjct: 760 QVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMIEV 818

Query: 703 PSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGA 762
           PSAALLA  LA+  DF S+GTNDL+QY LA+DR H  L+ + D LHPA+L+LI  T   A
Sbjct: 819 PSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAA 878

Query: 763 ARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQAL 822
             HG+WVGVCG LA+DPLA PVLVGLGV+ELSV    + E+K RVR+L  A+ +  AQA 
Sbjct: 879 HAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQAA 938

Query: 823 LDLGSARAVR 832
           L +GSA  VR
Sbjct: 939 LAVGSADDVR 948


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: 1923
Number of extensions: 109
Number of successful extensions: 5
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: 954
Length adjustment: 43
Effective length of query: 799
Effective length of database: 911
Effective search space:   727889
Effective search space used:   727889
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: 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