Alignments for a candidate for nagF in Desulfovibrio vulgaris Hildenborough

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 206413 DVU0981 multiphosphoryl transfer protein, putative

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



>MicrobesOnline__882:206413
          Length = 854

 Score =  409 bits (1052), Expect = e-118
 Identities = 306/826 (37%), Positives = 419/826 (50%), Gaps = 53/826 (6%)

Query: 65  VTLATAEGAEILLH-IGIDTVEL--------NGKGFAPMVAQGAHVRAGDVLIEFDQDQV 115
           V LA A G +   H IG D V +         G G   ++  G+ + + +  ++    +V
Sbjct: 29  VPLAVAGGIDDPDHPIGTDPVRVMTAIEEVQQGDGVLVLMDLGSALMSAETALDLLPPEV 88

Query: 116 A----LNAPSLV------SVIAIANSDAFEIVERVQGGLLKAGETPLL-----VLRARDG 160
           A    L+A  LV      +V+A   +D   + E  Q  L  A +  LL        A   
Sbjct: 89  ASQVRLSAAPLVEGLMAAAVLASTGADLGAVAEEAQSAL--AAKRELLGAAAPAAPAMPS 146

Query: 161 AAAEASRQLSSTNVTEEARQQVTLVHAG--GLHARPAARAREAARGFDARVEVRYEGRKA 218
           A  E +R  +  +    A +++TLV     GLHARPAAR   A   F A V++    R  
Sbjct: 147 AHPEGARDSTVPSSAMPAGEELTLVVPNRLGLHARPAARIVTALGPFAADVQLVRGDRVV 206

Query: 219 AIESVVGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAH-GEVEEKPARQSSPAP 277
           +  SV  +  L    G TV    +G  AA A+ AI  E    AH G+  E P++  +P+P
Sbjct: 207 SARSVNRIATLAVRGGETVTFRAVGGDAALALRAI--EALAAAHFGDAPEAPSKGEAPSP 264

Query: 278 --------QAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKAN--GTSAA 327
                    A A  + +      L G  A+PG+ VG  V W     D P+ A      A 
Sbjct: 265 AEAPKDGDMAEAAVSADVQGGGVLRGAAASPGLTVGNAV-WYRPAFDAPDVAPLADDPAT 323

Query: 328 ESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARD-LISLGK 386
           E   LD A+     +L    R         EA IF++HR+LL+D T+  AAR  ++   +
Sbjct: 324 EVTRLDAALGAARTELVELERRTVAAAGRKEAEIFAMHRLLLDDVTIAGAARQRIMDRRE 383

Query: 387 SAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLA 446
           +A  AW E I    A    + +  + ER AD+ D+  RVLR L   +A    L   +VL 
Sbjct: 384 AAESAWYEVISDAAATFRQLPEGYMREREADMVDVGARVLRLLTGVAAVGPRLGGPSVLL 443

Query: 447 AEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVV 506
           A +  PSD++TLD S V  +V  +GGATSHAAILAR  GIPA+  +G AL  + EG  V 
Sbjct: 444 ATDLGPSDMATLDPSLVIGIVTVQGGATSHAAILARSLGIPAVAGLGPALQGVGEGDIVA 503

Query: 507 VNATTGRLEFAPTELDVERARLERTRLADV--REANRRTSQQAAVTSDGRAIEVAANIAT 564
           ++  TG +   P      RA +E  R A +  REA    +   AVT+DGRA+ + ANI +
Sbjct: 504 LDGGTGDVWVNPAP--GVRAAVEARRDAWLAGREAALAGAAAPAVTADGRAVHILANIGS 561

Query: 565 LDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVG 624
             DA  A++NGA+ VGL RTE LF+ R + P  +E   +Y     A+ GR  ++RTLD+G
Sbjct: 562 SADAGAALKNGAEGVGLFRTEFLFLDRTSPPGEEEQLTAYVTAAAAMQGRPVVVRTLDIG 621

Query: 625 ADKEVDYLT--LPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTD 682
            DK V YL      E NP LGLRGIR    R  L   QLR LL    +  ++++ PMV  
Sbjct: 622 GDKPVSYLEGFATGEDNPFLGLRGIRFCLERKPLFMTQLRALLRAAAVHPLKVMFPMVAH 681

Query: 683 VGELIRIRKRIDEFARELGRTE----PIEVGVMIEVPSAALLADQLAQHADFLSIGTNDL 738
            GEL   +  +DE    L         ++VG+MIEVP+A  LADQLA+ A F SIGTNDL
Sbjct: 682 PGELAAAKALLDEARATLDAEGMPHGQLDVGIMIEVPAAVALADQLARDAAFFSIGTNDL 741

Query: 739 TQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLV 798
            QY +A DR  A +AA +D LHPAVLR++  TV+     G  V +CG L G+P A+PLLV
Sbjct: 742 AQYVMAADRGNASVAALSDALHPAVLRMVRDTVRAGHAAGIPVAICGELGGNPEAIPLLV 801

Query: 799 GLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVR 844
           GL + ELS++  ++P  K  VR  D   C   A  A+AL  A AVR
Sbjct: 802 GLELDELSMNGPAIPRAKEVVRGCDTGTCAVLADRAMALPDAAAVR 847


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: 1761
Number of extensions: 93
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: 854
Length of database: 854
Length adjustment: 42
Effective length of query: 812
Effective length of database: 812
Effective search space:   659344
Effective search space used:   659344
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: 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