Alignments for a candidate for bgl in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Sphingomonas koreensis DSMZ 15582

Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate Ga0059261_1166 Ga0059261_1166 Beta-glucosidase-related glycosidases

Query= reanno::Korea:Ga0059261_1166
         (834 letters)



>FitnessBrowser__Korea:Ga0059261_1166
          Length = 834

 Score = 1679 bits (4347), Expect = 0.0
 Identities = 834/834 (100%), Positives = 834/834 (100%)

Query: 1   MVPTGKPKLMFRLLSSAMLASLPVVMAATASARDDAAQAHPAMWPERRPTVPLDPAVELR 60
           MVPTGKPKLMFRLLSSAMLASLPVVMAATASARDDAAQAHPAMWPERRPTVPLDPAVELR
Sbjct: 1   MVPTGKPKLMFRLLSSAMLASLPVVMAATASARDDAAQAHPAMWPERRPTVPLDPAVELR 60

Query: 61  VADLLAKMSLEQKVGQIIQADIASVTPADVHRYHLGSVLNGGNSDPGGRYNAPPRDWLAA 120
           VADLLAKMSLEQKVGQIIQADIASVTPADVHRYHLGSVLNGGNSDPGGRYNAPPRDWLAA
Sbjct: 61  VADLLAKMSLEQKVGQIIQADIASVTPADVHRYHLGSVLNGGNSDPGGRYNAPPRDWLAA 120

Query: 121 ADAFYAASMQPNGALPRIPVIWGSDAVHGHNNVVGATLFPHNIGLGAARNPDLIRRIGEA 180
           ADAFYAASMQPNGALPRIPVIWGSDAVHGHNNVVGATLFPHNIGLGAARNPDLIRRIGEA
Sbjct: 121 ADAFYAASMQPNGALPRIPVIWGSDAVHGHNNVVGATLFPHNIGLGAARNPDLIRRIGEA 180

Query: 181 TAIEMRVTGLDWTFAPTLAVVRDDRWGRTYEGFGETPEIATAYAAPLIEGLQGKIGDKDW 240
           TAIEMRVTGLDWTFAPTLAVVRDDRWGRTYEGFGETPEIATAYAAPLIEGLQGKIGDKDW
Sbjct: 181 TAIEMRVTGLDWTFAPTLAVVRDDRWGRTYEGFGETPEIATAYAAPLIEGLQGKIGDKDW 240

Query: 241 LRGPHIIATAKHFLGDGGTRNGKDQGDTEIGEAGLRDLFSPPYLPALDAGVQSVMVSFSG 300
           LRGPHIIATAKHFLGDGGTRNGKDQGDTEIGEAGLRDLFSPPYLPALDAGVQSVMVSFSG
Sbjct: 241 LRGPHIIATAKHFLGDGGTRNGKDQGDTEIGEAGLRDLFSPPYLPALDAGVQSVMVSFSG 300

Query: 301 WNGAKMHGNKSLLTGVVKQRWNFDGFLVGDWNGHGQVAGCTATNCPQSAIAGLDMYMAPD 360
           WNGAKMHGNKSLLTGVVKQRWNFDGFLVGDWNGHGQVAGCTATNCPQSAIAGLDMYMAPD
Sbjct: 301 WNGAKMHGNKSLLTGVVKQRWNFDGFLVGDWNGHGQVAGCTATNCPQSAIAGLDMYMAPD 360

Query: 361 SWKALYEATLGQARDGTLPIDRLDDAVRRILRVKIRAGLFEAGKPSSRPYAGRYELLGSA 420
           SWKALYEATLGQARDGTLPIDRLDDAVRRILRVKIRAGLFEAGKPSSRPYAGRYELLGSA
Sbjct: 361 SWKALYEATLGQARDGTLPIDRLDDAVRRILRVKIRAGLFEAGKPSSRPYAGRYELLGSA 420

Query: 421 EHRALAREAVRQSLVLLKNANGLLPLKPGGRILVAGDGADNLTKQTGGWTLSWQGTGTQR 480
           EHRALAREAVRQSLVLLKNANGLLPLKPGGRILVAGDGADNLTKQTGGWTLSWQGTGTQR
Sbjct: 421 EHRALAREAVRQSLVLLKNANGLLPLKPGGRILVAGDGADNLTKQTGGWTLSWQGTGTQR 480

Query: 481 SDFPNAQSIWEGIEATVKAAGGTATLSVEGGYSAKPDAAIVVFGEEPYAEFQGDRPDVGY 540
           SDFPNAQSIWEGIEATVKAAGGTATLSVEGGYSAKPDAAIVVFGEEPYAEFQGDRPDVGY
Sbjct: 481 SDFPNAQSIWEGIEATVKAAGGTATLSVEGGYSAKPDAAIVVFGEEPYAEFQGDRPDVGY 540

Query: 541 DDAKTLALLRTLKTAGVPTVAVFLSGRAMWVNPFLNASDAFVAAWLPGSEGGGVADVLFG 600
           DDAKTLALLRTLKTAGVPTVAVFLSGRAMWVNPFLNASDAFVAAWLPGSEGGGVADVLFG
Sbjct: 541 DDAKTLALLRTLKTAGVPTVAVFLSGRAMWVNPFLNASDAFVAAWLPGSEGGGVADVLFG 600

Query: 601 KSDFSGKLGYSWPRSSDQTTVNIGDSNYDPLFPYGFGLKVADRGDLAALPETRATAAAAE 660
           KSDFSGKLGYSWPRSSDQTTVNIGDSNYDPLFPYGFGLKVADRGDLAALPETRATAAAAE
Sbjct: 601 KSDFSGKLGYSWPRSSDQTTVNIGDSNYDPLFPYGFGLKVADRGDLAALPETRATAAAAE 660

Query: 661 TGILFTAGKPGGGRRLLLGRPGELAANPGPELIDARPADRSAQEDSLRIRWTGAGQAVAA 720
           TGILFTAGKPGGGRRLLLGRPGELAANPGPELIDARPADRSAQEDSLRIRWTGAGQAVAA
Sbjct: 661 TGILFTAGKPGGGRRLLLGRPGELAANPGPELIDARPADRSAQEDSLRIRWTGAGQAVAA 720

Query: 721 IVQDVPVDLSRQANGDLALELELKVNAAPSAEVSLLMRCGTDCAGGFPVRGILGEAAKTG 780
           IVQDVPVDLSRQANGDLALELELKVNAAPSAEVSLLMRCGTDCAGGFPVRGILGEAAKTG
Sbjct: 721 IVQDVPVDLSRQANGDLALELELKVNAAPSAEVSLLMRCGTDCAGGFPVRGILGEAAKTG 780

Query: 781 KWTRVAVPLRCFEKAGVDMTRVETPLSIATAGSLDLTLSSARITSPSGPQLACK 834
           KWTRVAVPLRCFEKAGVDMTRVETPLSIATAGSLDLTLSSARITSPSGPQLACK
Sbjct: 781 KWTRVAVPLRCFEKAGVDMTRVETPLSIATAGSLDLTLSSARITSPSGPQLACK 834


Lambda     K      H
   0.317    0.135    0.412 

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: 2507
Number of extensions: 102
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: 834
Length of database: 834
Length adjustment: 42
Effective length of query: 792
Effective length of database: 792
Effective search space:   627264
Effective search space used:   627264
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: 56 (26.2 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