Aligments for a candidate for dhaM in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for dhaM in Escherichia coli BW25113

Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate 15320 b1198 fused predicted dihydroxyacetone-specific PTS enzymes: HPr component/EI component (RefSeq)

Query= BRENDA::P37349
         (472 letters)



>lcl|FitnessBrowser__Keio:15320 b1198 fused predicted
           dihydroxyacetone-specific PTS enzymes: HPr component/EI
           component (RefSeq)
          Length = 472

 Score =  917 bits (2370), Expect = 0.0
 Identities = 472/472 (100%), Positives = 472/472 (100%)

Query: 1   MVNLVIVSHSSRLGEGVGELARQMLMSDSCKIAIAAGIDDPQNPIGTDAVKVMEAIESVA 60
           MVNLVIVSHSSRLGEGVGELARQMLMSDSCKIAIAAGIDDPQNPIGTDAVKVMEAIESVA
Sbjct: 1   MVNLVIVSHSSRLGEGVGELARQMLMSDSCKIAIAAGIDDPQNPIGTDAVKVMEAIESVA 60

Query: 61  DADHVLVMMDMGSALLSAETALELLAPEIAAKVRLCAAPLVEGTLAATVSAASGADIDKV 120
           DADHVLVMMDMGSALLSAETALELLAPEIAAKVRLCAAPLVEGTLAATVSAASGADIDKV
Sbjct: 61  DADHVLVMMDMGSALLSAETALELLAPEIAAKVRLCAAPLVEGTLAATVSAASGADIDKV 120

Query: 121 IFDAMHALEAKREQLGLPSSDTEISDTCPAYDEEARSLAVVIKNRNGLHVRPASRLVYTL 180
           IFDAMHALEAKREQLGLPSSDTEISDTCPAYDEEARSLAVVIKNRNGLHVRPASRLVYTL
Sbjct: 121 IFDAMHALEAKREQLGLPSSDTEISDTCPAYDEEARSLAVVIKNRNGLHVRPASRLVYTL 180

Query: 181 STFNADMLLEKNGKCVTPESINQIALLQVRYNDTLRLIAKGPEAEEALIAFRQLAEDNFG 240
           STFNADMLLEKNGKCVTPESINQIALLQVRYNDTLRLIAKGPEAEEALIAFRQLAEDNFG
Sbjct: 181 STFNADMLLEKNGKCVTPESINQIALLQVRYNDTLRLIAKGPEAEEALIAFRQLAEDNFG 240

Query: 241 ETEEVAPPTLRPVPPVSGKAFYYQPVLCTVQAKSTLTVEEEQDRLRQAIDFTLLDLMTLT 300
           ETEEVAPPTLRPVPPVSGKAFYYQPVLCTVQAKSTLTVEEEQDRLRQAIDFTLLDLMTLT
Sbjct: 241 ETEEVAPPTLRPVPPVSGKAFYYQPVLCTVQAKSTLTVEEEQDRLRQAIDFTLLDLMTLT 300

Query: 301 AKAEASGLDDIAAIFSGHHTLLDDPELLAAASELLQHEHCTAEYAWQQVLKELSQQYQQL 360
           AKAEASGLDDIAAIFSGHHTLLDDPELLAAASELLQHEHCTAEYAWQQVLKELSQQYQQL
Sbjct: 301 AKAEASGLDDIAAIFSGHHTLLDDPELLAAASELLQHEHCTAEYAWQQVLKELSQQYQQL 360

Query: 361 DDEYLQARYIDVDDLLHRTLVHLTQTKEELPQFNSPTILLAENIYPSTVLQLDPAVVKGI 420
           DDEYLQARYIDVDDLLHRTLVHLTQTKEELPQFNSPTILLAENIYPSTVLQLDPAVVKGI
Sbjct: 361 DDEYLQARYIDVDDLLHRTLVHLTQTKEELPQFNSPTILLAENIYPSTVLQLDPAVVKGI 420

Query: 421 CLSAGSPVSHSALIARELGIGWICQQGEKLYAIQPEETLTLDVKTQRFNRQG 472
           CLSAGSPVSHSALIARELGIGWICQQGEKLYAIQPEETLTLDVKTQRFNRQG
Sbjct: 421 CLSAGSPVSHSALIARELGIGWICQQGEKLYAIQPEETLTLDVKTQRFNRQG 472


Lambda     K      H
   0.316    0.132    0.368 

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: 812
Number of extensions: 26
Number of successful extensions: 1
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: 472
Length of database: 472
Length adjustment: 33
Effective length of query: 439
Effective length of database: 439
Effective search space:   192721
Effective search space used:   192721
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 (21.6 bits)
S2: 51 (24.3 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 preprint 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