Alignments for a candidate for bgl in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Klebsiella michiganensis M5al

Align 6-P-β-glucosidase (BglA) (EC 3.2.1.21|3.2.1.86) (characterized)
to candidate BWI76_RS23855 BWI76_RS23855 6-phospho-beta-glucosidase

Query= CAZy::AAV37466.1
         (480 letters)



>FitnessBrowser__Koxy:BWI76_RS23855
          Length = 477

 Score =  767 bits (1981), Expect = 0.0
 Identities = 350/475 (73%), Positives = 409/475 (86%), Gaps = 3/475 (0%)

Query: 6   LPKDFLWGGAVAAHQVEGGWDQGGKGVSICDVLSGGAHGVDRVITDGVQPGVSYPNHQAV 65
           LPKDFLWGGAVAAHQVEGGW++ GKG SICDVL+GGAHGV R IT  V+PG  YPNH+A+
Sbjct: 6   LPKDFLWGGAVAAHQVEGGWNKDGKGPSICDVLTGGAHGVPREITQQVEPGKYYPNHEAI 65

Query: 66  EFYSHYKQDVALFAEMGFKCFRTSIAWTRIFPNGDELEPNEAGLQFYDDLFDELLKYNIE 125
           +F+  YK+D+ LFAEMGFKCFRTSIAWTRIFP GDE +PNE GL+FYDD+FDELLKYNIE
Sbjct: 66  DFHGRYKEDIKLFAEMGFKCFRTSIAWTRIFPLGDESQPNEEGLKFYDDMFDELLKYNIE 125

Query: 126 PVITLSHFEMPHHLVKQYGGWLNRKVVDFFVRYSEVVMKRYQSKVKYWMTFNEINNQRNW 185
           PVITLSHFEMP HLV+QYGGW NRKVVDFFVR++EVV +RY+ KVKYWMTFNEINNQRNW
Sbjct: 126 PVITLSHFEMPLHLVQQYGGWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEINNQRNW 185

Query: 186 QYPVFGYCCSGVIFTDHDKPEQAMYQTLHHQFVASAKVVKLGHEINPNFKIGCMLALVPI 245
           + P+FGYCCSGV++T+H+ PE+ MYQ LHHQFVASA  VK   +INP  ++GCMLA+VP+
Sbjct: 186 RAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAARQINPQMQVGCMLAMVPL 245

Query: 246 YPWSCHPDDVMFAQEAMRERHLFGDVQLRGYYPSYILKEWARKGYQIDMQPEDEQTLRDG 305
           YP+SC P+DVMFAQE+MRER++F DVQLRGYYPSY+L EW R+G+ I M+  D Q LR+G
Sbjct: 246 YPYSCKPEDVMFAQESMRERYVFTDVQLRGYYPSYVLNEWERRGFSIKMEDGDAQILREG 305

Query: 306 CTDYLGFSYYMSSAVQLAAKGQKKEDSITGFDGGVKNPHVKASEWGWQIDPVGLRYTLNS 365
              YLGFSYYM++AV+  A+G    D+I+GF+G V NPHVKAS+WGWQID VGLRY L  
Sbjct: 306 TCAYLGFSYYMTNAVK--AEG-GSGDAISGFEGSVPNPHVKASDWGWQIDSVGLRYALCE 362

Query: 366 FYERYQKPMFIVENGFGAVDKVEADGSINDDYRIEYLKAHIDQMKKTVVEDGVELMGYTP 425
            YERYQKP+FIVENGFGA DKVE DGSINDDYRI+YL+AH+++M K V  DGVELMGYTP
Sbjct: 363 LYERYQKPLFIVENGFGAYDKVEEDGSINDDYRIDYLRAHVEEMIKAVTYDGVELMGYTP 422

Query: 426 WGCIDCVSFTTGQYSKRYGFIYVDKHDDGTGTFKRSKKKSFDWYKKVISSNGAEL 480
           WGCIDCVSFTTGQYSKRYGFIYV+KHDDGTG   RS+KKSF+WYK VI+SNG +L
Sbjct: 423 WGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNWYKDVIASNGEKL 477


Lambda     K      H
   0.321    0.139    0.445 

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: 970
Number of extensions: 29
Number of successful extensions: 2
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: 480
Length of database: 477
Length adjustment: 34
Effective length of query: 446
Effective length of database: 443
Effective search space:   197578
Effective search space used:   197578
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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