GapMind for catabolism of small carbon sources

 

Alignments 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.

Links

Downloads

Related tools

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