GapMind for catabolism of small carbon sources

 

Alignments for a candidate for man-isomerase in Escherichia coli BW25113

Align uncharacterized sugar isomerase yihS (characterized)
to candidate 17920 b3880 orf, hypothetical protein (VIMSS)

Query= CharProtDB::CH_024519
         (413 letters)



>FitnessBrowser__Keio:17920
          Length = 413

 Score =  887 bits (2293), Expect = 0.0
 Identities = 413/413 (100%), Positives = 413/413 (100%)

Query: 1   MKWFNTLSHNRWLEQETDRIFDFGKNSVVPTGFGWLGNKGQIKEEMGTHLWITARMLHVY 60
           MKWFNTLSHNRWLEQETDRIFDFGKNSVVPTGFGWLGNKGQIKEEMGTHLWITARMLHVY
Sbjct: 1   MKWFNTLSHNRWLEQETDRIFDFGKNSVVPTGFGWLGNKGQIKEEMGTHLWITARMLHVY 60

Query: 61  SVAAAMGRPGAYSLVDHGIKAMNGALRDKKYGGWYACVNDEGVVDASKQGYQHFFALLGA 120
           SVAAAMGRPGAYSLVDHGIKAMNGALRDKKYGGWYACVNDEGVVDASKQGYQHFFALLGA
Sbjct: 61  SVAAAMGRPGAYSLVDHGIKAMNGALRDKKYGGWYACVNDEGVVDASKQGYQHFFALLGA 120

Query: 121 ASAVTTGHPEARKLLDYTIEIIEKYFWSEEEQMCLESWDEAFSKTEEYRGGNANMHAVEA 180
           ASAVTTGHPEARKLLDYTIEIIEKYFWSEEEQMCLESWDEAFSKTEEYRGGNANMHAVEA
Sbjct: 121 ASAVTTGHPEARKLLDYTIEIIEKYFWSEEEQMCLESWDEAFSKTEEYRGGNANMHAVEA 180

Query: 181 FLIVYDVTHDKKWLDRAIRVASVIIHDVARNNHYRVNEHFDTQWNPLPDYNKDNPAHRFR 240
           FLIVYDVTHDKKWLDRAIRVASVIIHDVARNNHYRVNEHFDTQWNPLPDYNKDNPAHRFR
Sbjct: 181 FLIVYDVTHDKKWLDRAIRVASVIIHDVARNNHYRVNEHFDTQWNPLPDYNKDNPAHRFR 240

Query: 241 AFGGTPGHWIEWGRLMLHIHAALEARCEQPPAWLLEDAKGLFNATVRDAWAPDGADGIVY 300
           AFGGTPGHWIEWGRLMLHIHAALEARCEQPPAWLLEDAKGLFNATVRDAWAPDGADGIVY
Sbjct: 241 AFGGTPGHWIEWGRLMLHIHAALEARCEQPPAWLLEDAKGLFNATVRDAWAPDGADGIVY 300

Query: 301 TVDWEGKPVVRERVRWPIVEAMGTAYALYTVTGDRQYETWYQTWWEYCIKYLMDYENGSW 360
           TVDWEGKPVVRERVRWPIVEAMGTAYALYTVTGDRQYETWYQTWWEYCIKYLMDYENGSW
Sbjct: 301 TVDWEGKPVVRERVRWPIVEAMGTAYALYTVTGDRQYETWYQTWWEYCIKYLMDYENGSW 360

Query: 361 WQELDADNKVTTKVWDGKQDIYHLLHCLVIPRIPLAPGMAPAVAAGLLDINAK 413
           WQELDADNKVTTKVWDGKQDIYHLLHCLVIPRIPLAPGMAPAVAAGLLDINAK
Sbjct: 361 WQELDADNKVTTKVWDGKQDIYHLLHCLVIPRIPLAPGMAPAVAAGLLDINAK 413


Lambda     K      H
   0.321    0.136    0.457 

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: 1007
Number of extensions: 37
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: 413
Length of database: 413
Length adjustment: 31
Effective length of query: 382
Effective length of database: 382
Effective search space:   145924
Effective search space used:   145924
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 (21.8 bits)
S2: 50 (23.9 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