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 (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate 349867 BT0339 alpha-glucosidase (NCBI ptt file)

Query= CAZy::AAO75446.1
         (748 letters)



>FitnessBrowser__Btheta:349867
          Length = 748

 Score = 1581 bits (4093), Expect = 0.0
 Identities = 748/748 (100%), Positives = 748/748 (100%)

Query: 1   MKPTNYHLFDFLDFDTELLRDESLWKACKPTAVYEKDGDICVTVPFQKQLLANDMVADTA 60
           MKPTNYHLFDFLDFDTELLRDESLWKACKPTAVYEKDGDICVTVPFQKQLLANDMVADTA
Sbjct: 1   MKPTNYHLFDFLDFDTELLRDESLWKACKPTAVYEKDGDICVTVPFQKQLLANDMVADTA 60

Query: 61  VPREEYTLIIRQYNIGITRLFLGFGEYELTDQSEMLQFSERIRRVPLSVEKQGGKWILFT 120
           VPREEYTLIIRQYNIGITRLFLGFGEYELTDQSEMLQFSERIRRVPLSVEKQGGKWILFT
Sbjct: 61  VPREEYTLIIRQYNIGITRLFLGFGEYELTDQSEMLQFSERIRRVPLSVEKQGGKWILFT 120

Query: 121 QDGTKRAVINVEEPALDRWSELLPDPQETLDITLYPDGKREIRLAAYDHFSPPRYDGLPI 180
           QDGTKRAVINVEEPALDRWSELLPDPQETLDITLYPDGKREIRLAAYDHFSPPRYDGLPI
Sbjct: 121 QDGTKRAVINVEEPALDRWSELLPDPQETLDITLYPDGKREIRLAAYDHFSPPRYDGLPI 180

Query: 181 AFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYKNI 240
           AFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYKNI
Sbjct: 181 AFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYKNI 240

Query: 241 PFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDL 300
           PFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDL
Sbjct: 241 PFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDL 300

Query: 301 TGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWK 360
           TGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWK
Sbjct: 301 TGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWK 360

Query: 361 FNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDGSN 420
           FNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDGSN
Sbjct: 361 FNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDGSN 420

Query: 421 FSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVYKGMKPELLNN 480
           FSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVYKGMKPELLNN
Sbjct: 421 FSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVYKGMKPELLNN 480

Query: 481 LYALLYQKAAYEITKEVTGDGIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKGGLHF 540
           LYALLYQKAAYEITKEVTGDGIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKGGLHF
Sbjct: 481 LYALLYQKAAYEITKEVTGDGIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKGGLHF 540

Query: 541 GLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPWHYPAI 600
           GLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPWHYPAI
Sbjct: 541 GLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPWHYPAI 600

Query: 601 APLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFGNDFL 660
           APLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFGNDFL
Sbjct: 601 APLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFGNDFL 660

Query: 661 VAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIPIYPE 720
           VAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIPIYPE
Sbjct: 661 VAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIPIYPE 720

Query: 721 EVNCTDEMDLGKSIALRIDHNYKGFWTK 748
           EVNCTDEMDLGKSIALRIDHNYKGFWTK
Sbjct: 721 EVNCTDEMDLGKSIALRIDHNYKGFWTK 748


Lambda     K      H
   0.322    0.139    0.449 

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: 2272
Number of extensions: 79
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: 748
Length of database: 748
Length adjustment: 40
Effective length of query: 708
Effective length of database: 708
Effective search space:   501264
Effective search space used:   501264
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: 55 (25.8 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