Alignments for a candidate for bgl in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Stenotrophomonas chelatiphaga DSM 21508

Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate WP_083492001.1 ABB28_RS10755 glycosyl hydrolase

Query= reanno::Caulo:CCNA_01019
         (758 letters)



>NCBI__GCF_001431535.1:WP_083492001.1
          Length = 928

 Score =  699 bits (1803), Expect = 0.0
 Identities = 374/730 (51%), Positives = 474/730 (64%), Gaps = 21/730 (2%)

Query: 14  LISASASALSVVPALADAAKPAAALAHPWMDKSLDADKRADLVLKAMTNDEKFTLIFGYF 73
           L  AS  AL     LA      A  + PWMD +L AD+R  L+L  MT DEKF ++  YF
Sbjct: 195 LRDASGKALKA-QLLALPYAQGATPSQPWMDTTLGADERTRLLLGEMTQDEKFQMLRSYF 253

Query: 74  GA--DMKPKYTRIPESLPGSAGYIAGVPRLGIPAQFQTDAGVGVATQGSAKEFRERTALP 131
           G   D  P    +PE   GSAG++ GV RLGIPAQ   DAGVGV   G  ++    TA+P
Sbjct: 254 GLGKDGGP----LPEGAVGSAGFVPGVARLGIPAQQSADAGVGVTNPGGIRKGDFATAMP 309

Query: 132 SGMATTATWNPELAFQGGAMIGKEARDSGFNVQLAGGVNLVREPRNGRNFEYGGEDPLLA 191
           SG +T ++WNP +A+ GGA +G+EA    FN+ L G VNL R+PRNGRNFEY GEDPLL 
Sbjct: 310 SGPSTASSWNPLIAYVGGATMGREAWQQRFNILLGGSVNLQRDPRNGRNFEYAGEDPLLG 369

Query: 192 GVMVAAQIRGIQSNNIISTIKHYALNAQETGRFVVSSNIDDTAARMSDLLAFQFAIEQSD 251
           GV+V   IRGIQS ++IST+KHYALN  ET R   S  I D A   SDLLAF+ AIE   
Sbjct: 370 GVIVGESIRGIQSQHVISTMKHYALNDMETRRNFHSVQIGDQAMHESDLLAFEIAIELGK 429

Query: 252 PHSVMCAYNRVNSVYACESDWLLNTVLKKDWGYKGYVMSDWGAAHSSAKAANAGLDQESA 311
           P S MC+YN++N +Y CE  +L+N VLK++W + G+VMSDWG  HS +KAA AGLDQ+SA
Sbjct: 430 PGSAMCSYNKINGIYGCEHPYLMNQVLKQEWKFPGFVMSDWGGVHSGSKAALAGLDQQSA 489

Query: 312 GDAFDKQPFFAAPLKADLASGAVSQARIDDMARRVLRAMFASGVVDHPLTGAPLAMPAET 371
           G+ FD   FF  PL+  +A G V QAR+DDM  R+LR MF  G  D+P    P+ + A  
Sbjct: 490 GEVFDATTFFDQPLRLAVAGGTVPQARLDDMVSRILRTMFLHGNFDNPPQHQPIDVEAGY 549

Query: 372 LAAHAKITQADAEEGIVLLKNDGGLLPLAKTAKTIAVIGSYADVGVLSGGGSSQ--VYPV 429
            AA     Q   EEG VLL+N+G LLPLA + K I +IG +AD GV+ GGGSS   V   
Sbjct: 550 AAA-----QRTVEEGSVLLRNEGNLLPLADSVKRIVIIGGHADKGVIGGGGSSMVGVTAK 604

Query: 430 GGRAVQGLEPKTWPGPVIYYPSSPLKAIAARYPGAKVVYDDGTDPARAAKLAASSDLALV 489
           G  AV G+ P TWPGPVI++PSSPL+A+ A  P A++ Y DG +PA AA+ AA +D+ALV
Sbjct: 605 GTNAVPGVMPTTWPGPVIFHPSSPLEALRAERPDAQITYVDGRNPAAAARAAAQADVALV 664

Query: 490 FADQWTTESVDVTTLNLPKNQDATIDAVASANKKTVVVLLTGGPLLMPWLDKVGAVVEAW 549
           FA QW+ ESVD+  + LP  QDA I AVA AN KTVVVL T GP+  PWL +V A+++AW
Sbjct: 665 FATQWSAESVDLPDMQLPDQQDALISAVAKANPKTVVVLETNGPVRTPWLAQVPALLQAW 724

Query: 550 FPGTAGGEAIARVLTGEVDASGRLPVTFPKSVAELPRPKLDGLG----KPDGEMFDVDYT 605
           +PG  GGE IA +LTG+V+ SGRLPVT+    ++LPRP + GLG    +P  ++FD D  
Sbjct: 725 YPGIRGGEGIAALLTGKVNPSGRLPVTWVVDESQLPRPHVPGLGFNPKQPAVDIFDFD-- 782

Query: 606 LEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFAYSNLTASASGDTLTVSFEVKNVGRRPGK 665
           +EGA VGYKW   K + P FAFGHGLSY+ FAY NL  S  G  +  S +V+N G R G 
Sbjct: 783 IEGANVGYKWAAAKGLVPTFAFGHGLSYSSFAYENLQVSVEGQRVVASVDVRNTGARAGA 842

Query: 666 DVPQVYVGPKAGGWEAPKRLAGFQKVSLAPGASQRVTVTVDPRLLAVWDSKAHGWSIAAG 725
           DV Q+Y+     G   P RL GF KV+L PG  +R+ +  +P+ LA +D  A  W IAAG
Sbjct: 843 DVAQLYL-KLPQGHTTPIRLVGFDKVNLQPGEQRRIRIEAEPKTLADFDPTAREWKIAAG 901

Query: 726 QYDIALGASS 735
            Y + LG ++
Sbjct: 902 TYQLQLGRNA 911


Lambda     K      H
   0.316    0.131    0.385 

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: 1654
Number of extensions: 81
Number of successful extensions: 6
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: 758
Length of database: 928
Length adjustment: 42
Effective length of query: 716
Effective length of database: 886
Effective search space:   634376
Effective search space used:   634376
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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