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 / glucoamylase (SusB;BtGH97a;BT3703;BT_3703) (EC 3.2.1.3) (characterized)
to candidate 354107 BT4581 alpha-glucosidase (NCBI ptt file)

Query= CAZy::AAC44671.1
         (738 letters)



>FitnessBrowser__Btheta:354107
          Length = 719

 Score = 1092 bits (2824), Expect = 0.0
 Identities = 523/742 (70%), Positives = 606/742 (81%), Gaps = 30/742 (4%)

Query: 1   MKKRKILSLIAFLCI--SFIANAQ---QKLTSPDNNLVMTFQVDSKGAPTYELTYKNKVV 55
           MK  KIL+  A LC+  SF   A    + +TSPD  L + F V+ +G P YELTYK K V
Sbjct: 1   MKNMKILTT-AVLCLLLSFSMGATAMAESITSPDGQLKLDFSVNVQGEPVYELTYKGKGV 59

Query: 56  IKPSTLGLELKKEDNTRTDFDWVDRRDLTKLDSKTNLYDGFEVKDTQTATFDETWQPVWG 115
           IKPS LGLELK +                       L +GF   DT+T+TFDETW+PVWG
Sbjct: 60  IKPSKLGLELKNDPG---------------------LMNGFACIDTKTSTFDETWEPVWG 98

Query: 116 EEKEIRNHYNELAVTLYQPMNDRSIVIRFRLFNDGLGFRYEFPQQKSLNYFVIKEEHSQF 175
           E K IRNHYNE+AVTL Q   DR+++IRFRL+NDGLGFRYEFPQQK+LNYFVIKEEHSQF
Sbjct: 99  EVKSIRNHYNEMAVTLNQKAQDRNMIIRFRLYNDGLGFRYEFPQQKNLNYFVIKEEHSQF 158

Query: 176 GMNGDHIAFWIPGDYDTQEYDYTISRLSEIRGLMKEAITPNSSQTPFSQTGVQTALMMKT 235
            M GDH AFWIPGDYDTQEYDYT SRL+EIRGLMK AIT N+SQT FS TGVQT+L MKT
Sbjct: 159 AMTGDHTAFWIPGDYDTQEYDYTESRLTEIRGLMKGAITDNASQTSFSPTGVQTSLQMKT 218

Query: 236 DDGLYINLHEAALVDYSCMHLNLDDKNMVFESWLTPDAKGDKGYMQTPCNTPWRTIIVSD 295
            DGLYINLHEAALVDYSCMHLNLDDK ++FESWLTPDA GDKGYMQTPC +PWRT+IVSD
Sbjct: 219 ADGLYINLHEAALVDYSCMHLNLDDKKLIFESWLTPDAMGDKGYMQTPCQSPWRTVIVSD 278

Query: 296 DARNILASRITLNLNEPCKIADAASWVKPVKYIGVWWDMITGKGSWAYTDELTSVKLGET 355
           DAR+ILAS++TLNLNEPC   D  SW+KPVKYIGVWW+MITGK SWAYTD++ SVKLG+T
Sbjct: 279 DARDILASKLTLNLNEPCAYQDV-SWIKPVKYIGVWWEMITGKSSWAYTDDVYSVKLGQT 337

Query: 356 DYSKTKPNGKHSANTANVKRYIDFAAAHGFDAVLVEGWNEGWEDWFGNSKDYVFDFVTPY 415
           DYSKT PNG+H+AN   VKRYIDFAA HGFD VLVEGWNEGWEDWFG SKDYVFDFVTPY
Sbjct: 338 DYSKTSPNGRHAANNDKVKRYIDFAAQHGFDQVLVEGWNEGWEDWFGKSKDYVFDFVTPY 397

Query: 416 PDFDVKEIHRYAARKGIKMMMHHETSASVRNYERHMDKAYQFMADNGYNSVKSGYVGNII 475
           PDFDVK ++ YA  KG+K+MMHHETSASVRNYERH+D AYQFM DNGYN+VKSGYVGNII
Sbjct: 398 PDFDVKMLNAYAKEKGVKLMMHHETSASVRNYERHLDTAYQFMVDNGYNAVKSGYVGNII 457

Query: 476 PRGEHHYGQWMNNHYLYAVKKAADYKIMVNAHEATRPTGICRTYPNLIGNESARGTEYES 535
           PRGEHHYGQWMNNHYLYAV KAADYKI VNAHEA RPTG+CRTYPNLIGNESARGTEYE+
Sbjct: 458 PRGEHHYGQWMNNHYLYAVTKAADYKICVNAHEAVRPTGLCRTYPNLIGNESARGTEYEA 517

Query: 536 FGGNKVYHTTILPFTRLVGGPMDYTPGIFETHCNKMNPANNSQVRSTIARQLALYVTMYS 595
           F GNK +HTT+LPFTR +GGPMDYTPGIF+T  + ++   +S VR+T+A+QLALYVTMYS
Sbjct: 518 FAGNKPFHTTLLPFTRQIGGPMDYTPGIFDTRISFLD-GKHSVVRTTLAKQLALYVTMYS 576

Query: 596 PLQMAADIPENYERFMDAFQFIKDVALDWDETNYLEAEPGEYITIARKAKDTDDWYVGCT 655
           PLQMAAD+PE+YER+ DAFQFIKDVALDWD++ YLEAEPG+YIT+ARKAK T+ W+VG  
Sbjct: 577 PLQMAADLPESYERYPDAFQFIKDVALDWDDSKYLEAEPGDYITVARKAKGTNHWFVGGI 636

Query: 656 AGENGHTSKLVFDFLTPGKQYIATVYADAKDADWKENPQAYTIKKGILTNKSKLNLHAAN 715
             EN  T+    DFL P K+Y+AT+YAD K+AD+++NP +Y IKKGI+TNK+K+++  A 
Sbjct: 637 TDENSRTAAFTLDFLEPDKEYVATLYADGKEADYEKNPTSYQIKKGIVTNKTKMSVKLAR 696

Query: 716 GGGYAISIKEVKDKSEAKGLKR 737
            GG+A+S+ E    S+ K +K+
Sbjct: 697 SGGFALSLIEAA-PSDRKSIKK 717


Lambda     K      H
   0.317    0.134    0.411 

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: 1954
Number of extensions: 98
Number of successful extensions: 4
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: 738
Length of database: 719
Length adjustment: 40
Effective length of query: 698
Effective length of database: 679
Effective search space:   473942
Effective search space used:   473942
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 (21.7 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)
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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