Alignments for a candidate for ascB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ascB in Klebsiella michiganensis M5al

Align 6-P-β-glucosidase (ChbF;ECs2440) (EC 3.2.1.86) (characterized)
to candidate BWI76_RS11745 BWI76_RS11745 6-phospho-beta-glucosidase

Query= CAZy::BAB35863.1
         (450 letters)



>FitnessBrowser__Koxy:BWI76_RS11745
          Length = 448

 Score =  793 bits (2049), Expect = 0.0
 Identities = 386/448 (86%), Positives = 419/448 (93%)

Query: 1   MSQKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKAKLDIIFDLCQRMID 60
           MSQKLKVVTIGGGSSYTPELLEGF+KRYHELP+SELWLVDV  G+ KLDII  LCQRM++
Sbjct: 1   MSQKLKVVTIGGGSSYTPELLEGFLKRYHELPISELWLVDVAEGQEKLDIIHALCQRMVE 60

Query: 61  NAGVPMKLYKTLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQETNGAGGLF 120
            AGVPMK+YKTLDRR AL+ ADFVTTQLRVGQL ARE DERIPLSHGYLGQETNGAGGLF
Sbjct: 61  KAGVPMKVYKTLDRRAALEGADFVTTQLRVGQLKAREKDERIPLSHGYLGQETNGAGGLF 120

Query: 121 KGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM 180
           KGLRTIPVIFDIVKDV+E+CPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM
Sbjct: 121 KGLRTIPVIFDIVKDVQEVCPNAWVINFTNPAGMVTEAVYRHTGFKRFIGVCNIPIGMKM 180

Query: 181 FIRDVLMLKDSDDLSIDLFGLNHMVFIKDVLVNGKSRFAELLDGVASGQLKASGVKNIFD 240
           FI DVL L  SD+L+IDLFGLNH+VF++DVLVNG SRF ELLDGVASG+L A+ VKNIFD
Sbjct: 181 FITDVLKLAPSDELNIDLFGLNHLVFVRDVLVNGVSRFDELLDGVASGRLSANSVKNIFD 240

Query: 241 LPFSEGLIRSLNLLPCSYLLYYFKQKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKNP 300
           LPFSEGL+RSL L+PCSYLLYYFK KEMLAIEMGEYYKGGARAQVVQKVEKQLFELYK+P
Sbjct: 241 LPFSEGLLRSLRLIPCSYLLYYFKPKEMLAIEMGEYYKGGARAQVVQKVEKQLFELYKDP 300

Query: 301 ELKVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNIPHHGHIDNIPADWAVEMTCT 360
           +L VKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVN+PHHGH+DNIPADWAVEMTCT
Sbjct: 301 DLNVKPKELEQRGGAYYSDAACEVINAIYNDKQAEHYVNVPHHGHVDNIPADWAVEMTCT 360

Query: 361 LGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALSGEFNDVLLALNLSPLVHSDRD 420
           LGRDGA P PRITHFD+KV+GLI+TIKGFE+AAS AA+SG+ +DVLLALNLSPL+HSDRD
Sbjct: 361 LGRDGAKPTPRITHFDEKVLGLIYTIKGFEVAASEAAISGKLDDVLLALNLSPLIHSDRD 420

Query: 421 AELLAREMILAHEKWLPNFADCIAELKK 448
           AE LAREMILAHE+WLPNFA  I +LK+
Sbjct: 421 AEKLAREMILAHEQWLPNFAATIEKLKQ 448


Lambda     K      H
   0.321    0.140    0.418 

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: 837
Number of extensions: 22
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: 448
Length adjustment: 33
Effective length of query: 417
Effective length of database: 415
Effective search space:   173055
Effective search space used:   173055
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 (21.9 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
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