Aligments for a candidate for nagF in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagF in Desulfovibrio vulgaris Hildenborough

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 206257 DVU0829 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>MicrobesOnline__882:206257
          Length = 590

 Score =  322 bits (826), Expect = 3e-92
 Identities = 200/571 (35%), Positives = 293/571 (51%), Gaps = 9/571 (1%)

Query: 288 LAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRL--LDKAIATVDADLDT 345
           +A   L G+  + G+++GK    D +            AAES +  LD+A A V +DLD 
Sbjct: 1   MARGILYGIAVSSGISIGKAFFMDRSRQSAAHDIIQPGAAESEVARLDEAAAQVASDLDR 60

Query: 346 TVRDASQRGAVGEAGIFSVHRVLLEDPTLL-DAARDLISLGKSAGFAWREAIRAQIAILT 404
             R          A I   HR++  DP L+ DAAR +     SA +A  +A+ A      
Sbjct: 61  A-RAQVPADLRDHAAIIDSHRMICRDPKLMGDAARRIREQNISAPWALEQAVDAIAQAFR 119

Query: 405 NIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVT 464
            I+D  + ER  D+R + +R+L  L   +   ++  E  VL A + TP+D   L  SR+ 
Sbjct: 120 AIDDPYIRERVQDVRAVAERILSRLAGNARELKSTGERMVLLAHDLTPADTIELQVSRIM 179

Query: 465 ALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVE 524
           +   A GG TSH  ILAR   IPA+V V     A  +G  V+++A  GR+   P E ++ 
Sbjct: 180 SFATAEGGKTSHTGILARSLQIPAVVGVSGLEEATADGDLVIIDALRGRILIDPDEHELA 239

Query: 525 RARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRT 584
                + +    + + RR S   A T DG  IEV +NI  L++    +++GAD VGL RT
Sbjct: 240 EYTELKYQFESYQRSIRRQSTLPAETLDGYRIEVQSNIELLEEVPQVLDSGADGVGLYRT 299

Query: 585 ELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGL 644
           E  F+ R   P+  +    Y  +   +S R  + RTLDVGADK +       EPNPALGL
Sbjct: 300 EYAFLARRQPPSEQDLCDEYSQVAALMSPRQVVFRTLDVGADKMLREQVRMEEPNPALGL 359

Query: 645 RGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELG--- 701
           R IR      D+   QLR +L     G V +L PM++ + EL + R  + E  +EL    
Sbjct: 360 RAIRFCLRHQDVFRTQLRAILRASVHGNVALLFPMISGIQELRQARHILQEVRQELDAEG 419

Query: 702 --RTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGL 759
                 + VG+M+E+PSA L+AD LA   DF SIGTNDL QY+L +DR    ++     L
Sbjct: 420 IPHAPDMPVGIMVELPSAVLIADALAHEVDFFSIGTNDLIQYSLGIDRGNRHVSYLYQPL 479

Query: 760 HPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARV 819
           HPA++R I   V  A + G  V VCG +A DP  +P+L+G+ +  +S+ P +VPGIK  +
Sbjct: 480 HPAIVRSIKLVVDSAHRAGISVSVCGEVASDPFCLPILMGMQIDSISIAPQAVPGIKHII 539

Query: 820 RNLDYQLCRQRAQDALALESAQAVRAASRET 850
           R  + + C+   +D L   +   +    +ET
Sbjct: 540 RKTNMEECKTLTRDVLNATTVSTINRMVKET 570


Lambda     K      H
   0.317    0.133    0.371 

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: 1018
Number of extensions: 41
Number of successful extensions: 3
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: 854
Length of database: 590
Length adjustment: 39
Effective length of query: 815
Effective length of database: 551
Effective search space:   449065
Effective search space used:   449065
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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, 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