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 β-glucosidase (Gluc3M) (EC 3.2.1.21) (characterized)
to candidate N515DRAFT_3995 N515DRAFT_3995 beta-glucosidase

Query= CAZy::ADC53302.1
         (831 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3995
          Length = 874

 Score =  278 bits (712), Expect = 7e-79
 Identities = 258/865 (29%), Positives = 374/865 (43%), Gaps = 134/865 (15%)

Query: 16  LLEELTLEEQVSLMAGADFWTTVPVPRLGIPAVKV-SDGPNGARGAGGLTNGTPAAAFPC 74
           L+  +TLEE+++ +  +       +PRLG+PA    S+G +G   AG  T       FP 
Sbjct: 45  LVARMTLEEKIAQLQSS----APAIPRLGVPAYDWWSEGLHGTARAGYAT------VFPQ 94

Query: 75  AIALGASWNRDAAYEMGAALAAEARSK------------GARVLLAPTVNMHRSGLNGRN 122
           AI L ASWN    +E+G  ++ EAR+K                + +P +N+ R    GR 
Sbjct: 95  AIGLAASWNAALLHEVGEVVSTEARAKYNLAGRGDHPRYHGLSIWSPNINIFRDPRWGRG 154

Query: 123 FECYSEDPLLTSMLAVAYVKGLQDNG-----VGATIKHFVANDS-EIDRQTVSSDVDERT 176
            E Y EDP LT  LA  +V+G+Q +        AT KHF  +   E  R    S      
Sbjct: 155 QETYGEDPFLTGTLATRFVRGIQGDDPAELKAAATPKHFAVHSGPEKGRHGFDSHTPPHD 214

Query: 177 LREIYLPPFEAAVKKAGVWAVMTGYNRLNGIHMDGHKWALQEVMRGEFGYDGIFMSDWFG 236
           L + YLP F  AV +    +VM  YN L G         LQE +R ++ + G  +SD   
Sbjct: 215 LEDTYLPAFRMAVTEGQAASVMCAYNALEGTPACASPLLLQERLRRDWRFAGYVVSDCDA 274

Query: 237 TN--------------SVAASVNAGHDLEMPGPTRYRGARLIDAVKAGEVDAETIRAAAR 282
            +              S AA+V AG DL+         A L +AV+ G+V    +  AAR
Sbjct: 275 VDDMTQFHHYKPDNAGSSAAAVAAGTDLDCG----IAYAALGEAVRKGQVSEAVLDQAAR 330

Query: 283 RLLVLFERVGAFHSA-GPEAETSR---DAPETRALIRRLGAEGAVLLKNEGNLLPLEKNV 338
           RL     R+G      GP A       ++P  RAL  R   E  VLLKNEG  LPL+++ 
Sbjct: 331 RLFAARYRMGMLDEPNGPYATLGAADINSPAHRALALRAARESIVLLKNEGGALPLKQDT 390

Query: 339 SIAALGPNAGVARLMGGGSAQINAPYRVTPVAGLKAAFGDNRVSHAKGCTNNRLTQVLQG 398
            IA +GPNA    ++   +    A   VTP+AGL+  FG  RVS+A+G T  +   V   
Sbjct: 391 RIAVIGPNADALNILEA-NYHGTAVDPVTPLAGLRKQFGAARVSYAQGATLAQGVSVPVP 449

Query: 399 DVELR--------------FHHGRRLEGKPVHIATEEALNCFWFDLPVPE-LDQNDFSVQ 443
              LR              F H     GKP  + T+  ++  W ++P  +     +++V+
Sbjct: 450 ASALRTGGKDAGPGLRGEYFDHAD-FNGKPRLVRTDHRIDFDWDEVPPAKGFAAANYAVR 508

Query: 444 VVATFTPEENGTYRAGM--------TNAGLARAYLDGELLIDGES-DWSHGQNFFGAAND 494
                 P   G Y   +              R Y+DG+L++D    D+        A   
Sbjct: 509 WTGDLLPPGAGDYNLNVHIDRCFDCKGHDPVRLYVDGKLVLDDHGKDYDLNVPLHFADTR 568

Query: 495 ERQVEIELQ-AGTTYQLVIDYCSPDSAENGITVRALRFGIEKTMGEQDIDDAVRLAGEQD 553
            R +++EL+ +G    + + + +P  A+                    + +A     + D
Sbjct: 569 PRPLKLELRHSGEDQGIRLQWNAPADAQ--------------------LREAKEAVAKAD 608

Query: 554 VAVLFVGRQEEWDSE----------GHDLPDMTLPGRQNALIEAVAAVNPNTVVVLQTGG 603
           V V  VG   + + E          G D  D+ LP  Q  L+EA  A     VVVL +G 
Sbjct: 609 VVVAVVGLSPDVEGEELQVSVPGFSGGDRTDLALPATQQKLLEAAKASGKPLVVVLTSGS 668

Query: 604 PVEMPWLDK-VKSVVQFWYPGQEVGNAIADVLSGAAYPGGRLPQTFPRRMKDNSAWSDDA 662
            V + W  +   ++V  WYPG+E G AIADVL+G   P GRLP TF              
Sbjct: 669 AVALNWAKQHADAIVAAWYPGEEGGTAIADVLAGNYNPAGRLPVTF-------------- 714

Query: 663 LTYPGKDGHVRYDEGVFVGYRHHDSRDVPPLFPFGFGLGYTRFDWGDAT-ADTAIMTDAG 721
             Y   D   ++D+    G  +   R   PLF FG GL YTRF +   T +   +     
Sbjct: 715 --YASADDLPKFDDYRMEGRTYRYFRGT-PLFAFGEGLSYTRFAYEAPTLSSKTLKAGDK 771

Query: 722 VTVTVPIVNSGAADGVEVVQLYVQPEAMVDDVPVARPKKELRAFARLALTPGEHGTASLG 781
           + V V + N+G  DG EVVQ+Y+             P+  L  F R+A   GE       
Sbjct: 772 LGVDVRVRNAGERDGDEVVQVYLSSS------EEGAPRHSLVGFRRVAFKAGESKLVHFE 825

Query: 782 IVPRDLAYFDVERQRWVAPAGRYTL 806
           I PR L+  +++ +R VAP G+Y L
Sbjct: 826 IDPRQLSVVNLKGERKVAP-GKYVL 849


Lambda     K      H
   0.317    0.135    0.406 

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: 1845
Number of extensions: 103
Number of successful extensions: 12
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: 831
Length of database: 874
Length adjustment: 42
Effective length of query: 789
Effective length of database: 832
Effective search space:   656448
Effective search space used:   656448
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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