Alignments for a candidate for bgl in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Paraburkholderia bryophila 376MFSha3.1

Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate H281DRAFT_00016 H281DRAFT_00016 beta-glucosidase

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



>FitnessBrowser__Burk376:H281DRAFT_00016
          Length = 763

 Score =  456 bits (1172), Expect = e-132
 Identities = 291/762 (38%), Positives = 415/762 (54%), Gaps = 42/762 (5%)

Query: 3   STTLRSLSLALLISASASALSVVPALA-DAAKPAAALAHPWMDKSLDADKRADLVLKAMT 61
           S  LR +    +  A  SA+SV   ++  A  P AA   PWM+ +L  ++RA L++ AM 
Sbjct: 7   SPHLRGIPHRAIRIACESAVSVAALVSLSAGAPQAASGPPWMNTALAPEQRAALLVGAMA 66

Query: 62  NDEKFTLIFGYFGADMKPKYTRIPESLPGSAGYIAGVPRLGIPAQFQTDAGVGVATQGSA 121
            D+K   + G  G         +P +   S  +I G+P L IP    T+  VG+      
Sbjct: 67  LDQKAAQLHGQSGT-----IAEVP-ACGNSIRHIPGIPALSIPTFRITNGPVGIGAGDCV 120

Query: 122 KEFRERTALPSGMATTATWNPELAFQGGAMIGKEARDSGFNVQLAGGVNLVREPRNGRNF 181
            + R  TALP  MA  A+++P LA   G ++G+EAR  G +V  A G+N VR  + GRNF
Sbjct: 121 PQDRA-TALPMSMALAASFDPTLARAYGDVLGREARMLGLHVVEAPGMNAVRVGQGGRNF 179

Query: 182 EYGGEDPLLAGVMVAAQIRGIQSNNIISTIKHYALNAQETGRFVVSSNIDDTAARMSDLL 241
           EY  EDP+LAGV+   +IRG Q+  +I+  KH+ LN QE  R  VS  +DD       LL
Sbjct: 180 EYLSEDPVLAGVIAENEIRGAQATGVIAMAKHFILNEQEANRNTVSVVVDDRTLHEIYLL 239

Query: 242 AFQFAIEQSDPHSVMCAYNRVNSVYACESDWLLNTVLKKDWGYKGYVMSDWGAAHSSAKA 301
            F  ++ + +  SVMC+YNR+ S YACE+   LN +L+ + G+ GYV SD+GA HS+A A
Sbjct: 240 PFGVSVRRGNVASVMCSYNRIGSTYACETPRALNAILRGELGFMGYVQSDFGATHSTAPA 299

Query: 302 ANAGLDQESAGDAFDKQPFFAAPLKADLASGAVSQARIDDMARRVLRAMFASGVVDHPLT 361
            NAGLD E     +    F    L A LA+G ++ A ++    R    MF +G+ D P+ 
Sbjct: 300 LNAGLDLEMQSGIW----FTPPNLNAALATGQLTMATVNQALTRRYTQMFKAGIFDRPVA 355

Query: 362 GAPLAMPAETLAAHAKITQADAEEGIVLLKNDGGLLPLAKTAKTIAVIG--SYADVGVLS 419
             PL   + T+       +   E+  VLLKN G LLPL+   K+I ++G  +Y D  +  
Sbjct: 356 RTPL--DSTTIQNDGTEARVIGEQSAVLLKNSGNLLPLSGAVKSITIVGHNTYVDDAIAG 413

Query: 420 GGGSSQVYPVGGRAVQGLEPKTWPGPVIYY--PSSPLKAIAARYPGAKVVYDDGTDPARA 477
           G GSS+V P        + P+     V+     S+ +K +AA         +DG+  A  
Sbjct: 414 GSGSSRVVP-----TYTVGPQQGITNVLRQLGSSATVKTLAAP--------NDGSMDAAV 460

Query: 478 AKLAASSDLALVFADQWTTESVDVTTLNLPKNQDATIDAVASANKKTVVVLLTGGPLLMP 537
           A  AA++D+A+V A   T E  D   L+LPK QD  I AVA+ N++T+VVL  G P+LMP
Sbjct: 461 AAAAATADVAIVMAGVVTGEGSDRPDLSLPKGQDKLIAAVANRNERTIVVLKDGDPVLMP 520

Query: 538 WLDKVGAVVEAWFPGTAGGEAIARVLTGEVDASGRLPVTFPKSVAELPRPKLDGLGKPDG 597
           W+D+V A++E W+ G   G  +AR+L G  + SG+LPVT+P+   + P    D      G
Sbjct: 521 WVDQVPAILETWYSGQEDGNVVARLLFGLANPSGKLPVTYPRLATDTPTSMPDRYPGTSG 580

Query: 598 EMFDVDYTLEGAAVGYKWYDLKKIEPLFAFGHGLSYTQFAYSNLTASASGDT----LTVS 653
               V Y+ EG  VGY+WYD ++++PLFAFGHGLSYT F  S++  S  G T    + V+
Sbjct: 581 SDPVVQYS-EGLLVGYRWYDTRQVKPLFAFGHGLSYTSFKISDVQVSPRGYTGNGPILVA 639

Query: 654 FEVKNVGRRPGKDVPQVYVGPKAGGWEAPKRLAGFQKVSLAPGASQRVTVTVDP----RL 709
             V+N G R G +V QVY+G      E  KRL  FQKV L PG  + +++ + P      
Sbjct: 640 LTVENTGLREGAEVAQVYLGLPPNLGEPTKRLIAFQKVLLKPGEKRALSMYIYPINGFHA 699

Query: 710 LAVWDSKAHGWSIAAGQYDIALGASSRAI--SSTAQVTLAAR 749
           L+ WD+ A  W IAAG Y + +G +S  I   ST  V +A R
Sbjct: 700 LSYWDNAAQSWKIAAGTYTVYVGNASDNIVAQSTFTVNVAMR 741


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: 1220
Number of extensions: 54
Number of successful extensions: 9
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: 763
Length adjustment: 40
Effective length of query: 718
Effective length of database: 723
Effective search space:   519114
Effective search space used:   519114
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: 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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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