Alignments for a candidate for fruI in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Desulfovibrio vulgaris Miyazaki F

Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate 8502167 DvMF_2877 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

Query= SwissProt::P45597
         (838 letters)



>FitnessBrowser__Miya:8502167
          Length = 591

 Score =  338 bits (867), Expect = 5e-97
 Identities = 211/573 (36%), Positives = 310/573 (54%), Gaps = 20/573 (3%)

Query: 271 AQPAIVGIGASPGVAIGIV----HRLRAAQTEVADQPIGLGDGGVL-LHDALTRTRQQLA 325
           A+  + GI  S GV+IG       R R+   E+   P G  D  V  L  A +  R  LA
Sbjct: 2   AREILQGIAVSAGVSIGKAFFTNRRRRSVSFEII--PPGAADSEVARLEQAASDVRDDLA 59

Query: 326 AIQDDTQRRLGASDAAIFKAQAELLNDTDLITRTCQLMVEGHGVA-WSWHQAVEQIASGL 384
             +D+    L    AAI  +   +  D  LI    Q + + H  A W+  QAVE IA+  
Sbjct: 60  RARDNVPAEL-RDHAAIINSHMMICQDPKLIRAASQRIRDHHICAEWALDQAVEAIAAAF 118

Query: 385 AALGNPVLAGRAADLRDVGRRVLAQLDPAAAGAGLTDLPEQPCILLAGDLSPSDTANLDT 444
           +A+ +P +  R  D+R V  R+  +L    A    T  P++  +L+A DL+P+D   L T
Sbjct: 119 SAIEDPYIRERVQDVRAVAERIQTRLVGRHAEPLRT--PDERIVLMAHDLTPADAMGLPT 176

Query: 445 DCVLGLATAQGGPTSHTAILSRTLGLPALVAAGGQLLDIEDGVTAIIDGSSGRLYINPSE 504
             ++  ATA+GG TSHT IL+R+L +PA+V        + DG   I+D   G + ++P E
Sbjct: 177 VKIMSFATAEGGKTSHTGILARSLQIPAVVGVSSLEESVADGDLVIVDALRGLIVVDPDE 236

Query: 505 LDLDAARTHIAEQ-QAIREREAAQRALPAETTDGHHIDIGANVNLPEQVAMALTQGAEGV 563
            +L A  T +  Q +  ++    Q  LPAET DG+ ID+ AN+ L E+V   L  G +GV
Sbjct: 237 TEL-ADYTDLKYQFENYQKSIRRQSTLPAETLDGYRIDVQANIELVEEVPQVLDGGGDGV 295

Query: 564 GLMRTEFLFLERGSTPTEDEQYQTYLAMARALDGRPLIVRALDIGGDKQVAHLELPHEEN 623
           GL RTE+ FL R ++PTE+E Y  Y  +A  L  R ++ R LD+G DK ++      E N
Sbjct: 296 GLYRTEYAFLNRRTSPTEEELYDEYSQLAGLLSPRRVVFRTLDVGADKMLSEQSQLEEPN 355

Query: 624 PFLGVRGARLLLRRPDLLEPQLRALYRAAKDGARLSIMFPMITSVPELISLREICARIRA 683
           P LG+R  R  LR  D+   QLRA+ RA+  G+  S++FPMI+ + EL   + I   +RA
Sbjct: 356 PALGLRAIRFCLRHQDVFRRQLRAILRASAHGS-ASLLFPMISGLHELRQAKHILNEVRA 414

Query: 684 ELDA------PELPIGIMIEVPAAAAQADVLARHADFFSIGTNDLTQYVLAIDRQNPELA 737
           ELDA      P++P+GIM+E+P+A   ++ LA+  DFFSIGTNDL QY L IDR N  ++
Sbjct: 415 ELDAAGLPYDPDMPVGIMVELPSAVMISEALAQEVDFFSIGTNDLIQYSLGIDRGNKHVS 474

Query: 738 AEADSLHPAVLRMIRSTIDGARKHDRWVGVCGGLAGDPFGASLLAGLGVQELSMTPNDIP 797
                LHPA++R I+  +D A +    V VCG +A DP+   +L G+ +  +S+ P  IP
Sbjct: 475 YLYQPLHPAIVRSIKYVVDSAHRMGISVCVCGEVASDPYCLPILLGMQIDAISIAPQAIP 534

Query: 798 AVKARLRGRALSALQQLAEQALQCETAEQVRAL 830
            +K  LR   +   ++L    L   T   +  +
Sbjct: 535 GIKHILRRTNMEECKELLRDVLSASTVSTINRM 567


Lambda     K      H
   0.318    0.134    0.385 

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: 1040
Number of extensions: 60
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: 838
Length of database: 591
Length adjustment: 39
Effective length of query: 799
Effective length of database: 552
Effective search space:   441048
Effective search space used:   441048
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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