GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Escherichia coli BW25113

Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)

Query= SwissProt::P20966
         (563 letters)



>FitnessBrowser__Keio:16276
          Length = 563

 Score = 1087 bits (2811), Expect = 0.0
 Identities = 563/563 (100%), Positives = 563/563 (100%)

Query: 1   MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK 60
           MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK
Sbjct: 1   MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK 60

Query: 61  NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF 120
           NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF
Sbjct: 61  NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF 120

Query: 121 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM 180
           MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM
Sbjct: 121 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM 180

Query: 181 YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM 240
           YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM
Sbjct: 181 YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM 240

Query: 241 VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT 300
           VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT
Sbjct: 241 VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT 300

Query: 301 PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV 360
           PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV
Sbjct: 301 PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV 360

Query: 361 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG 420
           GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG
Sbjct: 361 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG 420

Query: 421 LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP 480
           LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP
Sbjct: 421 LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP 480

Query: 481 FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG 540
           FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG
Sbjct: 481 FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG 540

Query: 541 TLVAGLAYAFLKRPEVDAVAKAA 563
           TLVAGLAYAFLKRPEVDAVAKAA
Sbjct: 541 TLVAGLAYAFLKRPEVDAVAKAA 563


Lambda     K      H
   0.320    0.136    0.392 

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: 1216
Number of extensions: 57
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: 563
Length of database: 563
Length adjustment: 36
Effective length of query: 527
Effective length of database: 527
Effective search space:   277729
Effective search space used:   277729
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: 53 (25.0 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:

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