Alignments for a candidate for nagF in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Rhodobacter johrii JA192

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 WP_108222992.1 C8J29_RS00705 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HXN5
         (842 letters)



>NCBI__GCF_003046325.1:WP_108222992.1
          Length = 838

 Score =  450 bits (1158), Expect = e-130
 Identities = 284/671 (42%), Positives = 377/671 (56%), Gaps = 37/671 (5%)

Query: 185 GLHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEA 244
           GLHARPA    + A+ F  +  +    + A   +++ ++GLG+   D + V   G+ +  
Sbjct: 175 GLHARPATEWAEAARRFPCRIRIRHGAEAADARNMISLLGLGLKSGDAITVSAEGQGAAE 234

Query: 245 ALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAG---------TLAGVCASPGLASG 295
           AL AL   +   +A    DA RA    E  R  A AG          + GV A+PGLA G
Sbjct: 235 ALAALKVTMTGLSAREKADAARA---EEKRRATAAAGGWVPPSSPRAVEGVPAAPGLAIG 291

Query: 296 PLARLGAISLPADDGRHRPEEQ----------HLALDQALQRVRDDVQGSLQQARLGGDE 345
            + R+      A DG   P+E           H AL Q  +++      + +  RLG  E
Sbjct: 292 RITRI------ATDGMEIPDEPVELARAADLLHAALGQTAEQLHSLADDTAR--RLG--E 341

Query: 346 NEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERAN 405
           ++AAIF A   LL DP L+  A   + +G G A +WHRA +     L AL N +LA RA 
Sbjct: 342 SDAAIFRAQAGLLADPDLITLASQWLVEGHGLAWSWHRAYEDMAARLSALRNPVLAARAA 401

Query: 406 DLRDLEKRVLRVLLGDTAPLRV---PAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGAT 462
           DLRD+ +R+L  +    A  R+   P G I+ A +I+PSD A L  A  AGL  A GG T
Sbjct: 402 DLRDVGQRLLAHIDPRFARSRLADLPEGTILVAEDISPSDAAGLDPAKVAGLVTALGGPT 461

Query: 463 SHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQRE 522
           SH AILAR+ GLP +V  G  +  LE+G + ++D   GRL L P    L      +A  E
Sbjct: 462 SHTAILARTLGLPAVVGTGPVVERLEDGARAIVDGHGGRLYLDPSEADLASARDWIAAEE 521

Query: 523 EQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAA 582
            +R R        A TRDG RI+IGAN+    +AA A   GA+GVGL+RTEFLFLER  +
Sbjct: 522 ARRARAAEARALPATTRDGHRIDIGANINLAEQAAFALGQGAEGVGLMRTEFLFLERSES 581

Query: 583 PDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARP 642
           P E+EQ  AY  +  A+  R ++IR +D+GGDK + +L LP EENP LG+RG  L   RP
Sbjct: 582 PTEDEQAEAYAAMARALDGRPLVIRALDIGGDKQVAHLDLPREENPFLGVRGARLLLRRP 641

Query: 643 ELLDQQLRALLRVEP-LERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIE 701
           +LL  QLRAL R      +  ++ PMV+ + EL  +R     +  +L    +P LG+M+E
Sbjct: 642 DLLVPQLRALYRAAAGGAQISVMFPMVTSLGELLELRAICERIRQELDAPVVP-LGIMVE 700

Query: 702 VPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAG 761
           VPSAALLA + A HADF SIGTNDL+QYALA+DR +  LA   D+LHPA+LRLI  T  G
Sbjct: 701 VPSAALLAAEFAAHADFFSIGTNDLTQYALAIDRQNPQLAPEADSLHPAVLRLIDLTVKG 760

Query: 762 AARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQA 821
           AA HGRWVGVCG +A DP    +L GLGV+ELS+ P  +  +K R+RQ D A  R  A+ 
Sbjct: 761 AAVHGRWVGVCGGIAGDPFGAALLAGLGVDELSMTPRDIPAVKERLRQSDRAGLRALAER 820

Query: 822 LLDLGSARAVR 832
            L    A AVR
Sbjct: 821 ALACSDAEAVR 831


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: 1746
Number of extensions: 95
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: 838
Length adjustment: 42
Effective length of query: 800
Effective length of database: 796
Effective search space:   636800
Effective search space used:   636800
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 24 2021. The underlying query database was built on Sep 17 2021.

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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 2024 update 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