Aligments for a candidate for ascB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for ascB in Escherichia coli BW25113

Align 6-P-β-glucosidase (CelF) (EC 3.2.1.86) (characterized)
to candidate 15852 b1734 cryptic phospho-beta-glucosidase, NAD(P)-binding (NCBI)

Query= CAZy::AAC74804.1
         (450 letters)



>lcl|FitnessBrowser__Keio:15852 b1734 cryptic
           phospho-beta-glucosidase, NAD(P)-binding (NCBI)
          Length = 450

 Score =  908 bits (2347), Expect = 0.0
 Identities = 450/450 (100%), Positives = 450/450 (100%)

Query: 1   MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMID 60
           MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMID
Sbjct: 1   MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMID 60

Query: 61  NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF 120
           NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF
Sbjct: 61  NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF 120

Query: 121 KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM 180
           KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM
Sbjct: 121 KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM 180

Query: 181 FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLINGKSRFAELLDGVASGQLKASSVKNIFD 240
           FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLINGKSRFAELLDGVASGQLKASSVKNIFD
Sbjct: 181 FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLINGKSRFAELLDGVASGQLKASSVKNIFD 240

Query: 241 LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP 300
           LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP
Sbjct: 241 LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP 300

Query: 301 ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGQIDNIPADWAVEMTCK 360
           ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGQIDNIPADWAVEMTCK
Sbjct: 301 ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGQIDNIPADWAVEMTCK 360

Query: 361 LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD 420
           LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD
Sbjct: 361 LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD 420

Query: 421 AELLAREMILAHEKWLPNFADCIAELKKAH 450
           AELLAREMILAHEKWLPNFADCIAELKKAH
Sbjct: 421 AELLAREMILAHEKWLPNFADCIAELKKAH 450


Lambda     K      H
   0.321    0.140    0.417 

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: 940
Number of extensions: 29
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 paper from 2022 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