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-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate PfGW456L13_953 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_953
          Length = 759

 Score =  278 bits (711), Expect = 8e-79
 Identities = 203/628 (32%), Positives = 313/628 (49%), Gaps = 26/628 (4%)

Query: 222 IMGLGVAEQDEVEVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAG 281
           ++G+ V +Q E      GE  EA L  + A LA   A A  +A  +I             
Sbjct: 121 VVGVLVIQQKERRQFDEGE--EAFLVTMSAQLAGVIAHA--EATGSIRGLGRQGKGIQEA 176

Query: 282 TLAGVCASPGLASGPLARLGAISLPADDGRHRPEEQHLALDQ-------ALQRVRDDVQG 334
              GV  SPG A G       + LP  D    P++    +D        A++ VR D++ 
Sbjct: 177 KFVGVPGSPGAAVGT----AVVMLPPADLDVVPDKTITDIDAELGLFKTAIEGVRADMRT 232

Query: 335 SLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQA 394
              +        E A+F  +L +L+D  L      +I  G  A  A  + +       + 
Sbjct: 233 LSAKLATQLRPEERALFDVYLMMLDDAALGSEVTTVIKTGQWAQGALRQVVTDHVNRFEL 292

Query: 395 LGNLLLAERANDLRDLEKRVLRVLLGDTAPLRV-PAGAIVAAREITPSDLAPLVDAGAAG 453
           + +  L ERA+D++DL +R+L  L  +     V P   I+ + E+TP+ L  + +   AG
Sbjct: 293 MDDAYLRERASDVKDLGRRLLAYLQEERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAG 352

Query: 454 LCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQ 513
           L    G   SHVAILAR+ G+P ++ L        +G Q+++D   G +  +P     +Q
Sbjct: 353 LVSVLGSGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSEVLRKQ 412

Query: 514 VALQVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLR 571
            A  V   EE++     DA R+   +T DG R+ +  N     + A A   GA+GVGL R
Sbjct: 413 FAEVV--EEEKQLALGLDALRDLPCVTVDGHRMPLWVNTGLLADVARAQKRGAEGVGLYR 470

Query: 572 TEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALG 631
           TE  F+  +  P E+EQ   Y+E L A   + V +RT+D+GGDK L Y P+  E+NP LG
Sbjct: 471 TEVPFMINQRFPSEKEQLAIYREQLSAFHPQPVTMRTLDIGGDKSLSYFPIK-EDNPFLG 529

Query: 632 LRGIHLGQARPELLDQQLRALLRV-EPLERCRILLPMVSEVDELRA----IRRRLGELAT 686
            RGI +    PE+   Q RA+L+  E L   RILLPM+S   EL      I R  GE+  
Sbjct: 530 WRGIRVTLDHPEIFLVQTRAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRD 589

Query: 687 QLGIERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDA 746
           +     +P +GVMIE+P+A     +LA   DFLS+G+NDL+QY LA+DR +  +AD  D 
Sbjct: 590 EGCDVPMPPIGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDY 649

Query: 747 LHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTR 806
           LHPA+L+ +      A   G+ V +CG +A DP A  +L+ +G + LS+    + ++K  
Sbjct: 650 LHPAVLQALQNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWM 709

Query: 807 VRQLDAAECRRHAQALLDLGSARAVRDA 834
           +RQ++ ++ R     L+ + + + +  +
Sbjct: 710 LRQINLSKARELLAELMTIDNPQVIHSS 737


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: 1307
Number of extensions: 69
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: 842
Length of database: 759
Length adjustment: 41
Effective length of query: 801
Effective length of database: 718
Effective search space:   575118
Effective search space used:   575118
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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