Alignments for a candidate for nagF in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Dechlorosoma suillum PS

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate Dsui_0742 Dsui_0742 phosphoenolpyruvate-protein phosphotransferase

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



>FitnessBrowser__PS:Dsui_0742
          Length = 579

 Score =  293 bits (749), Expect = 3e-83
 Identities = 192/544 (35%), Positives = 289/544 (53%), Gaps = 17/544 (3%)

Query: 292 TLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLL--DKAIATVDADLDTTVRD 349
           T+ G+  + G+A+G       A ++      G   A+  +L  + AI  V A+L+    +
Sbjct: 4   TIHGLGVSGGIAIGVAQLMSHATLEVAHLTIGPRMADKEVLRFEAAILAVQAELEQLKLE 63

Query: 350 ASQRGAVGEAGIF-SVHRVLLEDPTLLDAARDLISLGK-SAGFAWREAIRAQIAILTNIE 407
           AS+  A  E   F  +H ++L DP L +  + +I   + +A +A  + +   +A    I+
Sbjct: 64  ASKGNAPAELRAFVDLHGMILADPELSEVPKQIIRERRCNAEWAVVQQMERLVAQFDAID 123

Query: 408 DALLAERAADLRDIEKRVLRAL----GYTSATARTLPEEA---VLAAEEFTPSDLSTLDR 460
           DA L ER AD+  + +RV++ L    G ++  AR   +E    ++ A + +P+D      
Sbjct: 124 DAYLRERKADVVQVVERVVKVLMGHPGRSALRARKGGKETTDQIIVAHDLSPADTIGFKE 183

Query: 461 SRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTE 520
            R  + +   GGATSH AILAR   IP++V +  A   I +G  ++++ T G +   P E
Sbjct: 184 QRFASFITDVGGATSHTAILARSMAIPSIVGLHRARDLIRDGELLIIDGTRGVVIVNPDE 243

Query: 521 LDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVG 580
             +E  RL ++ L   R   +R     A T DG  + + ANI   +D + A   GAD +G
Sbjct: 244 RVLEEYRLRKSELELERSKLKRLKTMKATTLDGVDVLMYANIELPEDVEAARTAGADGIG 303

Query: 581 LLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNP 640
           L RTE LF++R   PT DE  ++Y+ +V  + G+   IRT D+GADK +D +    + NP
Sbjct: 304 LFRTEFLFLNRGDMPTEDEQFEAYRKVVKGMEGKPVTIRTFDLGADKALDAMD-RVKTNP 362

Query: 641 ALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGEL---IRIRKRIDEFA 697
           ALGLR IRL    P +   QLR +L     G V+IL+PM+    E+   +   +   +  
Sbjct: 363 ALGLRAIRLQLAEPKMFRTQLRAILRASKYGKVKILIPMLAHAHEIDATLAAVQAAKQSL 422

Query: 698 RE--LGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQ 755
           RE  +G  E IEVG MIE+P+AAL      +  DFLSIGTNDL QY LA+DR    ++  
Sbjct: 423 REQKIGFDEGIEVGGMIEIPAAALAIGMFLRRLDFLSIGTNDLIQYALAIDRSDETVSQL 482

Query: 756 ADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGI 815
            D LHPAVL L+A T+   +K G  V VCG LAGDP    LL+G+G+   S+ P  +  +
Sbjct: 483 YDPLHPAVLMLVAHTIYSGEKAGLPVSVCGELAGDPAMTRLLLGMGLRVFSMHPSQILEV 542

Query: 816 KARV 819
           K  V
Sbjct: 543 KQHV 546


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: 975
Number of extensions: 37
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: 579
Length adjustment: 39
Effective length of query: 815
Effective length of database: 540
Effective search space:   440100
Effective search space used:   440100
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: 54 (25.4 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