Alignments for a candidate for bgl in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Dyella japonica UNC79MFTsu3.2

Align macrolide β-glycosidase / β-glucosidase (DesR) (EC 3.2.1.21|3.2.1.-) (characterized)
to candidate N515DRAFT_3995 N515DRAFT_3995 beta-glucosidase

Query= CAZy::ACR54627.1
         (828 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3995
          Length = 874

 Score =  257 bits (657), Expect = 2e-72
 Identities = 267/891 (29%), Positives = 373/891 (41%), Gaps = 176/891 (19%)

Query: 12  RGRTTP---RAFTLAVVGTLLAGTTVAAAAPGAADTANVQYTSRAAELVAQMTLDEKISF 68
           R R  P   R      +G   AG  VA  A         Q   RAAELVA+MTL+EKI+ 
Sbjct: 6   RSRVRPLRFRRLAALALGLACAGHAVAMDA--------AQAERRAAELVARMTLEEKIA- 56

Query: 69  VHWALDPDRQNVGYLPGVPRLGIPELRA-ADGPNGIRLVGQTATALPAPVALASTFDDTM 127
                    Q     P +PRLG+P     ++G +G    G  AT  P  + LA++++  +
Sbjct: 57  ---------QLQSSAPAIPRLGVPAYDWWSEGLHGTARAGY-ATVFPQAIGLAASWNAAL 106

Query: 128 ADSYGKVMGRDGRA------------LNQDMVLGPMMNNIRVPHGGRNYETFSEDPLVSS 175
               G+V+  + RA             +   +  P +N  R P  GR  ET+ EDP ++ 
Sbjct: 107 LHEVGEVVSTEARAKYNLAGRGDHPRYHGLSIWSPNINIFRDPRWGRGQETYGEDPFLTG 166

Query: 176 RTAVAQIKGIQGAG-----LMTTAKHFAANN-QENNRFSVNANVDEQTLREIEFPAFEAS 229
             A   ++GIQG          T KHFA ++  E  R   +++     L +   PAF  +
Sbjct: 167 TLATRFVRGIQGDDPAELKAAATPKHFAVHSGPEKGRHGFDSHTPPHDLEDTYLPAFRMA 226

Query: 230 SKAG-AASFMCAYNGLNGKPSCGNDELLNNVLRTQWGFQGWVMSDWLAT----------- 277
              G AAS MCAYN L G P+C +  LL   LR  W F G+V+SD  A            
Sbjct: 227 VTEGQAASVMCAYNALEGTPACASPLLLQERLRRDWRFAGYVVSDCDAVDDMTQFHHYKP 286

Query: 278 ----PGTDAITKGLDQEMGVELPGDVPKGEPSPPAKFFGEALKTAVLNGTVPEAAVTRSA 333
                   A+  G D + G+                    AL  AV  G V EA + ++A
Sbjct: 287 DNAGSSAAAVAAGTDLDCGIAY-----------------AALGEAVRKGQVSEAVLDQAA 329

Query: 334 ERIVGQMEKFGLLLATPAP-----RPERDKAGAQAVSRKVAENGAVLLRNEGQALPLAGD 388
            R+     + G+L     P       + +    +A++ + A    VLL+NEG ALPL  D
Sbjct: 330 RRLFAARYRMGMLDEPNGPYATLGAADINSPAHRALALRAARESIVLLKNEGGALPLKQD 389

Query: 389 AGKSIAVIGPTAVDPKVTGLGSAHVVPDSAAAPLDTIKARAGAGATVTYETG---EETFG 445
               IAVIGP A D       + H        PL  ++ + GA A V+Y  G    +   
Sbjct: 390 T--RIAVIGPNA-DALNILEANYHGTAVDPVTPLAGLRKQFGA-ARVSYAQGATLAQGVS 445

Query: 446 TQIPAGNLSPAFNQGHQLEPGKAGALYD-------------------------------- 473
             +PA  L      G    PG  G  +D                                
Sbjct: 446 VPVPASALRTG---GKDAGPGLRGEYFDHADFNGKPRLVRTDHRIDFDWDEVPPAKGFAA 502

Query: 474 --------GTLTVPADGEYRIAVRA-----TGGYATVQL---GSHTIEAGQVYGKVSSPL 517
                   G L  P  G+Y + V         G+  V+L   G   ++       ++ PL
Sbjct: 503 ANYAVRWTGDLLPPGAGDYNLNVHIDRCFDCKGHDPVRLYVDGKLVLDDHGKDYDLNVPL 562

Query: 518 LKLTKGTHKLTISGFAMSATPLSLELGWVTPAAADATIAEAVESARKAR--TAVVFAYDD 575
                    L +     S     + L W  P  ADA + EA E+  KA    AVV    D
Sbjct: 563 HFADTRPRPLKLE-LRHSGEDQGIRLQWNAP--ADAQLREAKEAVAKADVVVAVVGLSPD 619

Query: 576 -----------GTEGVDRPNLSLPGTQDKLISAVADANPNTIVVLNTGSSVLMPWLSK-T 623
                      G  G DR +L+LP TQ KL+ A   +    +VVL +GS+V + W  +  
Sbjct: 620 VEGEELQVSVPGFSGGDRTDLALPATQQKLLEAAKASGKPLVVVLTSGSAVALNWAKQHA 679

Query: 624 RAVLDMWYPGQAGAEATAALLYGDVNPSGKLTQSFPAAENQHAVAGDPTSYPGVDNQQTY 683
            A++  WYPG+ G  A A +L G+ NP+G+L  +F A+ +           P  D+ +  
Sbjct: 680 DAIVAAWYPGEEGGTAIADVLAGNYNPAGRLPVTFYASAD---------DLPKFDDYR-- 728

Query: 684 REGIHVGYRWFDKENVKPLFPFGHGLSYTSFTQSAPTV-VRTSAGG--LKVTVTVRNSGK 740
            EG    YR+F      PLF FG GLSYT F   APT+  +T   G  L V V VRN+G+
Sbjct: 729 MEG--RTYRYF---RGTPLFAFGEGLSYTRFAYEAPTLSSKTLKAGDKLGVDVRVRNAGE 783

Query: 741 RAGQEVVQAYLGASPNVTAPQAKKKLVGYTKVSLAAGEAKTVTVNVDRRQL 791
           R G EVVQ YL +S    AP  +  LVG+ +V+  AGE+K V   +D RQL
Sbjct: 784 RDGDEVVQVYLSSSEE-GAP--RHSLVGFRRVAFKAGESKLVHFEIDPRQL 831


Lambda     K      H
   0.313    0.130    0.379 

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: 1744
Number of extensions: 93
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 828
Length of database: 874
Length adjustment: 42
Effective length of query: 786
Effective length of database: 832
Effective search space:   653952
Effective search space used:   653952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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