GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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