Alignments for a candidate for nagF in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Caulobacter crescentus NA1000

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 CCNA_00457 CCNA_00457 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__Caulo:CCNA_00457
          Length = 852

 Score =  685 bits (1768), Expect = 0.0
 Identities = 400/842 (47%), Positives = 519/842 (61%), Gaps = 24/842 (2%)

Query: 5   NLALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALS 64
           NL L APL G V  L   PD VF+   LG+G+AIDPL   LHAPC G V  + R RHA++
Sbjct: 5   NLVLTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRARHAVT 64

Query: 65  LRADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVM 124
           LRA NGAE+L+HVGL+TV L GEGFE  VEEG  V  G  L+  DLD +A+ +RSLIT +
Sbjct: 65  LRATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPV 124

Query: 125 ILTNGDGFQ-VRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHH 183
           ++TNG+ FQ VR      + VG  L++LSP     R A        A  Q+  +  V   
Sbjct: 125 VITNGEAFQIVRRDQDRQIGVGQFLMELSPIAGASRAA-----ASGAADQITRQIIVPLA 179

Query: 184 GGLHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSE 243
            G+HARPAA + + A+ F+S   L    + A+  S VG+M L +   D ++++  G D++
Sbjct: 180 HGIHARPAARIAQMAKTFASDLTLATGPRRANARSPVGLMSLAIRHGDTIQLLASGPDAQ 239

Query: 244 AALGALL---------AALASATAGAPKDAPRAIAPGEPARPAAVA--GTLAGVCASPGL 292
           AA+ AL           A  +A   + K AP    P EP  PA +   G L GV A+PGL
Sbjct: 240 AAVTALAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGVLKGVPAAPGL 299

Query: 293 ASGPLARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGDENEAAIFS 352
           A G   RL    +   +       +  AL  AL+ VR      + +A   GD+   AI +
Sbjct: 300 AIGKAVRLSTAEIVVREAGEGVAHEEAALAVALETVR----ARIGKAAETGDKARKAILA 355

Query: 353 AHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEK 412
           AH A L+DP L   A  LI +G  A  AW RA+    + LQALG+  +AER +DL DLE+
Sbjct: 356 AHQAFLDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVDDLIDLER 415

Query: 413 RVLRVLLGD--TAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILAR 470
           +VLR L G+  T     P G+I+ A E+ PS L     A  AG   A GG TSHVAILA 
Sbjct: 416 QVLRALSGEEETGAALAP-GSILLADELLPSQLMGADPAALAGFATARGGPTSHVAILAA 474

Query: 471 SKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQA 530
           + G+P LVA+G  L ++++G  ++LDA  G L ++PDA+ LE     +AQR++++   +A
Sbjct: 475 AMGVPALVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQRKAAAKA 534

Query: 531 DAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRN 590
            A   A+TRDG RIE+ AN  S  +A  A ANGA+G GLLRTEFLFL+R   PDE+EQ  
Sbjct: 535 AAHEPAVTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPDEDEQAR 594

Query: 591 AYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLR 650
            YQ + +A+  R +IIRT+DVGGDK   YLP+P EENPALGLRG+ +   RP LL  QLR
Sbjct: 595 QYQAIAEALDGRPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHLLKAQLR 654

Query: 651 ALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLAD 710
           A+LRVEP  +C+I++PMV+ +DELRA+R  L E   +LGI    +LGVMIE P+AA+ AD
Sbjct: 655 AILRVEPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPAAAVTAD 714

Query: 711 QLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVG 770
            LA  ADFLSIGTNDL+QY LAMDR +  LA  IDALHPA+LR+I QTC GAARH RWVG
Sbjct: 715 LLAAEADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAARHHRWVG 774

Query: 771 VCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARA 830
           VCG LASD  ATP+L+GLGV ELS   ++  ++K RVR L    CR  A   L+  S +A
Sbjct: 775 VCGGLASDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALEQTSPQA 834

Query: 831 VR 832
           VR
Sbjct: 835 VR 836


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: 1814
Number of extensions: 90
Number of successful extensions: 7
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: 852
Length adjustment: 42
Effective length of query: 800
Effective length of database: 810
Effective search space:   648000
Effective search space used:   648000
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
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