Alignments for a candidate for nagF in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Desulfovibrio vulgaris Miyazaki F

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

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



>FitnessBrowser__Miya:8501869
          Length = 846

 Score =  402 bits (1034), Expect = e-116
 Identities = 294/819 (35%), Positives = 407/819 (49%), Gaps = 37/819 (4%)

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

Query: 116 ALN-----APSLVSVIAIA-----NSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEA 165
           A       AP +  V+A A      +D   ++   Q  L    E   + L    G   EA
Sbjct: 89  AAQVRLRPAPLVEGVMAAAVQASIGADLDTVLREAQSALAAKAELLGMALPQDGGGVDEA 148

Query: 166 SRQLSSTNVTEEARQQVTLVHAG--GLHARPAARAREAARGFDARVEVRYEGRKAAIESV 223
           +    +   T  A  ++TL+     GLHARPAAR   A   F A V++    R  +  SV
Sbjct: 149 APP--AAGATPAASHELTLMVPNRLGLHARPAARIVTALGPFVADVQLARGERVVSARSV 206

Query: 224 VGLLGLGAGEGATVELLGMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARP 283
             +  L    G T+     G  A  A+ A+A +L  E  G++ +          +    P
Sbjct: 207 NRIATLAVRGGETITFRAAGTDAEQALKALA-DLAAENFGDLPDATKSSGRTGVEGPEGP 265

Query: 284 -----AGETLAPNTLAGVCAAPGVAVGKLVRWDDA-DIDPPEKANGTSAAESRLLDKAIA 337
                AG    P    GV A+PG+AVG  V    A D  PP+ A G   +E+  LD A+ 
Sbjct: 266 GEQGRAGVAGVPAAKGGVPASPGIAVGPAVWHRPAFDAPPPDLAAGDPDSEAARLDGALD 325

Query: 338 TVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKS-AGFAWREAI 396
               +L    R  +      EA IF +HR+LL+D T+   AR  I+  +  A  AW   I
Sbjct: 326 AARKELAALERRTAAMAGKQEAEIFVMHRLLLDDATIAGDARQRIAERREPAEAAWYAVI 385

Query: 397 RAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLS 456
                    + +  + ERAADL D+  RVLR L     +   L   +VL A +  PSD++
Sbjct: 386 DQAAESFRQLPEGYMRERAADLVDVGARVLRLLTGAPPSGPRLERPSVLLAADLGPSDMA 445

Query: 457 TLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEF 516
            LD + V  +V A+GGATSHAAILAR  GIPA+   G    ++ +G  V ++ +TG +  
Sbjct: 446 HLDPALVLGIVTAQGGATSHAAILARSMGIPAVAGAGALAASVADGVTVALDGSTGEVWI 505

Query: 517 APTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGA 576
           AP    +      R     VR+A    + + AVT DGR + V ANI +  DA  A++NGA
Sbjct: 506 APAPDVLSTIESRRASWLAVRQAALAGAARPAVTVDGRHMHVHANIGSPMDAAPALQNGA 565

Query: 577 DSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYL--TL 634
           + VGL RTE LF+ R AAP  +E R +Y A   A+ G   ++RTLD+G DK V YL    
Sbjct: 566 EGVGLFRTEFLFLDRVAAPDEEEQRAAYVAAAAAMPGLPVVVRTLDIGGDKPVPYLGDFA 625

Query: 635 PPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRID 694
             E NP LGLRGIR    R +L   QLR LL       +R++ PMV   GEL   +  ++
Sbjct: 626 AGEENPFLGLRGIRFCLARRELFLTQLRALLRAAAEHPLRVMFPMVAHPGELAAAKALLE 685

Query: 695 EFARELGRT----EPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQA 750
           E    L        P+EVG+M+EVP+A  LADQLA+ + F SIGTNDL QY +A DR  A
Sbjct: 686 EARAALAAQGLPHGPVEVGIMVEVPAAVALADQLARESAFFSIGTNDLAQYVMAADRGNA 745

Query: 751 DLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPV 810
            +A  +D LHPAVLR++  TV      G  V +CG LAG+  A+PLLVGLG+ ELS++  
Sbjct: 746 AVADLSDALHPAVLRMVRDTVAAGKAAGIPVAMCGELAGNADAIPLLVGLGLDELSMNGP 805

Query: 811 SVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAASRE 849
           ++P  K  VR  D   C + A  AL L  A AVR   R+
Sbjct: 806 AIPRAKDVVRGCDMTACVRLAGRALELPDAAAVRRLLRD 844


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: 1739
Number of extensions: 79
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: 846
Length adjustment: 42
Effective length of query: 812
Effective length of database: 804
Effective search space:   652848
Effective search space used:   652848
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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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