Alignments for a candidate for susB in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Bacteroides thetaiotaomicron VPI-5482

Align α-glucosidase (BT3299;BT_3299) (EC 3.2.1.20) (characterized)
to candidate 352826 BT3299 alpha-glucosidase II (NCBI ptt file)

Query= CAZy::AAO78405.1
         (683 letters)



>FitnessBrowser__Btheta:352826
          Length = 683

 Score = 1419 bits (3673), Expect = 0.0
 Identities = 683/683 (100%), Positives = 683/683 (100%)

Query: 1   MVGDGIAKFIPEGFDAQKIPSFAIEKEPREQGALPADWVLVPEFSLTDGKANASLTVPEG 60
           MVGDGIAKFIPEGFDAQKIPSFAIEKEPREQGALPADWVLVPEFSLTDGKANASLTVPEG
Sbjct: 1   MVGDGIAKFIPEGFDAQKIPSFAIEKEPREQGALPADWVLVPEFSLTDGKANASLTVPEG 60

Query: 61  TSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPWMMGVRKDGTAFGILFD 120
           TSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPWMMGVRKDGTAFGILFD
Sbjct: 61  TSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPWMMGVRKDGTAFGILFD 120

Query: 121 TTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELTGTMPMIPRWALGYQQC 180
           TTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELTGTMPMIPRWALGYQQC
Sbjct: 121 TTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELTGTMPMIPRWALGYQQC 180

Query: 181 RFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNPKSFPNPKAVNRDLHIR 240
           RFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNPKSFPNPKAVNRDLHIR
Sbjct: 181 RFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNPKSFPNPKAVNRDLHIR 240

Query: 241 GFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAWPGAAAFPDFTSPKVNK 300
           GFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAWPGAAAFPDFTSPKVNK
Sbjct: 241 GFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAWPGAAAFPDFTSPKVNK 300

Query: 301 WWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPEDNLHRGGGKLPAGTHLQYHNVYGF 360
           WWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPEDNLHRGGGKLPAGTHLQYHNVYGF
Sbjct: 301 WWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPEDNLHRGGGKLPAGTHLQYHNVYGF 360

Query: 361 LMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSCWDHLKMSVPMSLTLGL 420
           LMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSCWDHLKMSVPMSLTLGL
Sbjct: 361 LMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSCWDHLKMSVPMSLTLGL 420

Query: 421 SGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTNNKEPWVFGQKVEDASR 480
           SGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTNNKEPWVFGQKVEDASR
Sbjct: 421 SGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTNNKEPWVFGQKVEDASR 480

Query: 481 IALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAEEEAFLVGDNLLIIPAF 540
           IALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAEEEAFLVGDNLLIIPAF
Sbjct: 481 IALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAEEEAFLVGDNLLIIPAF 540

Query: 541 ANQPALPKGIWKELSLVEGDQNDKYQAKMKIRGGAIIPTGKIIQNTTENSLDPLTLLVCL 600
           ANQPALPKGIWKELSLVEGDQNDKYQAKMKIRGGAIIPTGKIIQNTTENSLDPLTLLVCL
Sbjct: 541 ANQPALPKGIWKELSLVEGDQNDKYQAKMKIRGGAIIPTGKIIQNTTENSLDPLTLLVCL 600

Query: 601 DEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLTKKTGKYNTENKDMAVI 660
           DEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLTKKTGKYNTENKDMAVI
Sbjct: 601 DEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLTKKTGKYNTENKDMAVI 660

Query: 661 KIITDQGIRQASGNLVEGIEIRL 683
           KIITDQGIRQASGNLVEGIEIRL
Sbjct: 661 KIITDQGIRQASGNLVEGIEIRL 683


Lambda     K      H
   0.319    0.138    0.434 

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: 2026
Number of extensions: 99
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: 683
Length of database: 683
Length adjustment: 39
Effective length of query: 644
Effective length of database: 644
Effective search space:   414736
Effective search space used:   414736
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 (21.7 bits)
S2: 54 (25.4 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)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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