Aligments for a candidate for fruI in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruI in Desulfovibrio vulgaris Hildenborough

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate 206257 DVU0829 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>MicrobesOnline__882:206257
          Length = 590

 Score =  325 bits (833), Expect = 5e-93
 Identities = 198/573 (34%), Positives = 310/573 (54%), Gaps = 28/573 (4%)

Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALAD-DTARRL 341
           GIA S G++IG    + R+  S   +   +I+ G    E   L     +  +D D AR  
Sbjct: 8   GIAVSSGISIGKAFFMDRSRQSAAHD---IIQPGAAESEVARLDEAAAQVASDLDRARAQ 64

Query: 342 GPSE----AAIFAAQAEILNDTDLVTLACQLMVEGH-GVAWSWHQAVERTAAGLAALDNP 396
            P++    AAI  +   I  D  L+  A + + E +    W+  QAV+  A    A+D+P
Sbjct: 65  VPADLRDHAAIIDSHRMICRDPKLMGDAARRIREQNISAPWALEQAVDAIAQAFRAIDDP 124

Query: 397 VLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTP--CILIAEDLSPSDTAALDMARVI 454
            +  R  D+R V +R+L+R+      G A +L  T    +L+A DL+P+DT  L ++R++
Sbjct: 125 YIRERVQDVRAVAERILSRL-----AGNARELKSTGERMVLLAHDLTPADTIELQVSRIM 179

Query: 455 GLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIA 514
             ATA+GG TSHT ILAR+L +PA+V         A+G   I+D   GR+ + P   ++A
Sbjct: 180 SFATAEGGKTSHTGILARSLQIPAVVGVSGLEEATADGDLVIIDALRGRILIDPDEHELA 239

Query: 515 DARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRT 574
           +      + E+ +     +  LPA T DG+ +E+ +N+   ++V   L  GA+ VGL RT
Sbjct: 240 EYTELKYQFESYQRSIRRQSTLPAETLDGYRIEVQSNIELLEEVPQVLDSGADGVGLYRT 299

Query: 575 EFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGV 634
           E+ FL R   P E +  + Y  +   +  R ++ R LD+G DK +       E NP LG+
Sbjct: 300 EYAFLARRQPPSEQDLCDEYSQVAALMSPRQVVFRTLDVGADKMLREQVRMEEPNPALGL 359

Query: 635 RGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRA 694
           R  R  LR  ++  TQLRA+ RA+  G       ++++FPMI+ + E++  R   + +R 
Sbjct: 360 RAIRFCLRHQDVFRTQLRAILRASVHGN------VALLFPMISGIQELRQARHILQEVRQ 413

Query: 695 ELD------APAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELA 748
           ELD      AP +P+GIMVE+P+A + AD LA  VDFFSIGTNDL QY+L IDR +  ++
Sbjct: 414 ELDAEGIPHAPDMPVGIMVELPSAVLIADALAHEVDFFSIGTNDLIQYSLGIDRGNRHVS 473

Query: 749 AEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIP 808
                LHPA++R I+L V+ A R G  V VCG +A DPF   +L G+ +  +S+ P+ +P
Sbjct: 474 YLYQPLHPAIVRSIKLVVDSAHRAGISVSVCGEVASDPFCLPILMGMQIDSISIAPQAVP 533

Query: 809 AVKDRLRGSDLSALKDAAQRALDCETADAVRAL 841
            +K  +R +++   K   +  L+  T   +  +
Sbjct: 534 GIKHIIRKTNMEECKTLTRDVLNATTVSTINRM 566


Lambda     K      H
   0.319    0.134    0.387 

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: 951
Number of extensions: 42
Number of successful extensions: 5
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: 846
Length of database: 590
Length adjustment: 39
Effective length of query: 807
Effective length of database: 551
Effective search space:   444657
Effective search space used:   444657
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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, 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