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 β-glucosidase (BglX) (EC 3.2.1.21) (characterized)
to candidate BWI76_RS19510 BWI76_RS19510 beta-glucosidase

Query= CAZy::AAA60495.1
         (789 letters)



>FitnessBrowser__Koxy:BWI76_RS19510
          Length = 765

 Score = 1418 bits (3671), Expect = 0.0
 Identities = 702/765 (91%), Positives = 740/765 (96%)

Query: 25  MKWLCSVGIAVSLALQPALADDLFGNHPLTPEARDAFVTELLKKMTVDEKIGQLRLISVG 84
           MKWLC+VG+AVSLALQPALAD+LFGNHPLTP+ARDAFVTELL KMTVDEKIGQLRLISVG
Sbjct: 1   MKWLCTVGVAVSLALQPALADELFGNHPLTPQARDAFVTELLTKMTVDEKIGQLRLISVG 60

Query: 85  PDNPKEAIREMIKDGQVGAIFNTVTRQDIRAMQDQVMELSRLKIPLFFAYDVLHGQRTVF 144
           PDNPKEAIREMIK+GQVGAIFNTVTR DIR MQDQVMELSRLKIPLFFAYDVLHGQRTVF
Sbjct: 61  PDNPKEAIREMIKEGQVGAIFNTVTRHDIRTMQDQVMELSRLKIPLFFAYDVLHGQRTVF 120

Query: 145 PISLGLASSFNLDAVKTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL 204
           PISLGLASSFNLDAV TVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL
Sbjct: 121 PISLGLASSFNLDAVNTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL 180

Query: 205 TSTMGKTMVEAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSPQRLFNDYMPPY 264
           T+ MG+ MVE+MQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSPQRLFNDYMPPY
Sbjct: 181 TTEMGRAMVESMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSPQRLFNDYMPPY 240

Query: 265 KAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDQWGFKGITVSDHGAIKELIKHGTA 324
           KAGLDAGSGAVMVALNSLNGTPATSD+WLLKDVLRDQWGFKGITVSDHGAIKELIKHG A
Sbjct: 241 KAGLDAGSGAVMVALNSLNGTPATSDAWLLKDVLRDQWGFKGITVSDHGAIKELIKHGVA 300

Query: 325 ADPEDAVRVALKSGINMSMSDEYYSKYLPGLIKSGKVTMAELDDAARHVLNVKYDMGLFN 384
           +DPEDAVRVALKSGINMSMSDEYYSKYLPGL+KSGKVTMAELDDA RHVLNVKYDMGLFN
Sbjct: 301 SDPEDAVRVALKSGINMSMSDEYYSKYLPGLVKSGKVTMAELDDATRHVLNVKYDMGLFN 360

Query: 385 DPYSHLGPKESDPVDTNAESRLHRKEAREVARESLVLLKNRLETLPLKKSATIAVVGPLA 444
           DPYSHLGPK+SDP DTNAESRLHRKEAREVARESLVLLKNRL+TLPLKKS TIAV+G LA
Sbjct: 361 DPYSHLGPKDSDPQDTNAESRLHRKEAREVARESLVLLKNRLDTLPLKKSGTIAVIGALA 420

Query: 445 DSKRDVMGSWSAAGVADQSVTVLTGIKNAVGENGKVLYAKGANVTSDKGIIDFLNQYEEA 504
           DSKRD+MGSWSAAGVA QSVTVLTG++NA+G+ GK+++AKGANVT DKGI+DFLN YE+A
Sbjct: 421 DSKRDMMGSWSAAGVAGQSVTVLTGMQNALGDKGKIIFAKGANVTDDKGIVDFLNLYEKA 480

Query: 505 VKVDPRSPQEMIDEAVQTAKQSDVVVAVVGEAQGMAHEASSRTDITIPQSQRDLIAALKA 564
           V+VD RSPQEMIDEAV  AKQSDVVVAVVGEAQGMAHEASSRTDIT+P SQR LI+ALKA
Sbjct: 481 VQVDSRSPQEMIDEAVAAAKQSDVVVAVVGEAQGMAHEASSRTDITLPPSQRALISALKA 540

Query: 565 TGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPMSFP 624
           TGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPMSFP
Sbjct: 541 TGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPMSFP 600

Query: 625 RSVGQIPVYYSHLNTGRPYNADKPNKYTSRYFDEANGALYPFGYGLSYTTFTVSDVKLSA 684
           RSVGQIP YYSHLNTGRPYNADKPNKYTSRYFDEANG LYPFGYGLSYTTF+VSDVK+SA
Sbjct: 601 RSVGQIPTYYSHLNTGRPYNADKPNKYTSRYFDEANGPLYPFGYGLSYTTFSVSDVKMSA 660

Query: 685 PTMKRDGKVTASVQVTNTGKREGATVVQMYLQDVTASMSRPVKQLKGFEKITLKPGETQT 744
           PT++RDGKVTASVQVTNTGKREGATV+Q+YLQDVTASMSRPVK L+GF+K+TLKPGETQT
Sbjct: 661 PTLQRDGKVTASVQVTNTGKREGATVIQLYLQDVTASMSRPVKMLRGFKKVTLKPGETQT 720

Query: 745 VSFPIDIEALKFWNQQMKYDAEPGKFNVFIGTDSARVKKGEFELL 789
           VSFPID+EALKFWNQQMKYDAEPGKFNVFIG DSARVK+ EFELL
Sbjct: 721 VSFPIDVEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQSEFELL 765


Lambda     K      H
   0.316    0.132    0.380 

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: 1903
Number of extensions: 51
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: 789
Length of database: 765
Length adjustment: 41
Effective length of query: 748
Effective length of database: 724
Effective search space:   541552
Effective search space used:   541552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 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