Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N2E3

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 AO353_05485 AO353_05485 PTS fructose transporter subunit IIA

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05485
          Length = 953

 Score =  456 bits (1173), Expect = e-132
 Identities = 279/668 (41%), Positives = 377/668 (56%), Gaps = 18/668 (2%)

Query: 177 RARVAHHGGLHARPAALLRKTAQGFSSQAELHFA-GQ--VASVDSLVGIMGLGVAEQDEV 233
           R  +A+  GLHARPA +L + A+ F  +  +    GQ    SV SL  ++ LG      +
Sbjct: 286 RIALANAHGLHARPAKILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQVL 345

Query: 234 EVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARP------AAVAG-TLAGV 286
           E+I     +  AL ALL A+        +  P   A  E          A  +G  +  V
Sbjct: 346 ELIAEPSIAADALPALLRAIEEGLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCVIQAV 405

Query: 287 CASPGLASGP--LARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGD 344
            A+PG+A GP  +  L AI  P        E + L    +L  VR D++G +Q+++    
Sbjct: 406 AAAPGIAIGPAHIQVLQAIDYPLRGESTAIERERLKT--SLADVRRDIEGLIQRSKAKAI 463

Query: 345 ENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERA 404
                IF  H  +L+DP L D  D  + QG  A  AW   I A     ++L + LLAERA
Sbjct: 464 RE---IFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERA 520

Query: 405 NDLRDLEKRVLRVLLGDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSH 464
            DLRD+ +RVL  L G   P       I+   E+ PSD+A L     AG+  A GGAT+H
Sbjct: 521 ADLRDIGRRVLAQLCGIETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAH 580

Query: 465 VAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQ 524
            AI+AR+ G+P LV  GA +L L  G  ++LD  +GRL +  DA  L++ A +   RE++
Sbjct: 581 SAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQR 640

Query: 525 RRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPD 584
            +   A   + ALT DG  +E+ AN+        A   GA+G+GLLRTE +F+  + APD
Sbjct: 641 LQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPD 700

Query: 585 EEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPEL 644
           E  Q   Y+ VLD +  R +++RT+DVGGDK L Y P+  EENP LG+RGI L   RP++
Sbjct: 701 EATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQI 760

Query: 645 LDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPS 704
           ++ QLRALLR       RI+ PMV  VDE R  R     L  ++ +  L +LG+MIEVPS
Sbjct: 761 MEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVADL-QLGIMIEVPS 819

Query: 705 AALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAAR 764
           AALLA  LA+  DF S+GTNDL+QY LA+DR H  L+ + D LHPA+L+LI  T   A  
Sbjct: 820 AALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHA 879

Query: 765 HGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLD 824
           HG+WVGVCG LA+DPLA PVLVGLGV+ELSV    +GE+K RVR+L  A+ +  AQ  L 
Sbjct: 880 HGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALA 939

Query: 825 LGSARAVR 832
           +GSA  VR
Sbjct: 940 VGSANEVR 947


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: 1904
Number of extensions: 101
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: 953
Length adjustment: 43
Effective length of query: 799
Effective length of database: 910
Effective search space:   727090
Effective search space used:   727090
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)
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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