Alignments for a candidate for bgl in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Echinicola vietnamensis KMM 6221, DSM 17526

Align β-glucosidase 3C (Sde_2674) (Bgl3C) (EC 3.2.1.21) (characterized)
to candidate Echvi_2675 Echvi_2675 Beta-glucosidase-related glycosidases

Query= CAZy::ABD81934.1
         (866 letters)



>FitnessBrowser__Cola:Echvi_2675
          Length = 906

 Score =  335 bits (859), Expect = 7e-96
 Identities = 265/857 (30%), Positives = 420/857 (49%), Gaps = 109/857 (12%)

Query: 60  EAEVERLLPLLTLEEKASLVHANSKFSIASIERLGIHEM-WMSDGPHGVRYQIERHGWAP 118
           E  V+ L+  ++LEEK S +   S     +I RL + E  W ++  HGV         A 
Sbjct: 60  EERVDILVDQMSLEEKVSQMMNASP----AIPRLKVPEYNWWNECLHGV---------AR 106

Query: 119 AGWTDDNSTYLPPLTTVAASWNPEIAALHGDVLGAEARHRRKDVILG------------- 165
           AG+    +T  P   +VAAS++  +    G V+  EAR +  + I               
Sbjct: 107 AGY----ATVFPQSISVAASFDKNLMKDIGSVISDEARAKHHEFIRNGKRGIYTGLDFWS 162

Query: 166 PGVNLARLPLYGRNFEYMGEDPFLASRLAVAEIKAIQEND-----VAACIKHFALNN-QE 219
           P +N+ R P +GR  E  GEDP+L   LA   I+ +Q++D       A  KHFA+++  E
Sbjct: 163 PNINIFRDPRWGRGHETYGEDPYLTGELASQFIEGLQDSDGKYLKTIATSKHFAVHSGPE 222

Query: 220 LNRTGVNAKPDERTLREVYLPAFEAAVKEAGVHTIMGAYNEFRGTNANQSKHLVMDILKG 279
             R   +    +R L E YLPAF   VKEA V++IMGAYN FRG + +    L+  +L+ 
Sbjct: 223 PLRHTFDVDVSDRDLYETYLPAFRKTVKEAKVYSIMGAYNRFRGESCSGHDFLLNQLLRE 282

Query: 280 EWGYKGVLLTDWNV--DINT--------YDAAVNGLDIEMGTNVDSYDDYMLAQPMIDMI 329
           +WG++G +++D     DI+T         +AA  G+      N  +Y  ++      + +
Sbjct: 283 QWGFEGYVVSDCGAIQDIHTGHKIASTAAEAAAIGVSGGCDLNCGNYYTHLT-----EAV 337

Query: 330 KAGSIPESVLDDKVRRILRVQLSIGMMDKYRLSGERN-------TAKHHEAARKIASEGI 382
             G I E  +D  V+R+   +  +GM D                +  H+  AR+ A + +
Sbjct: 338 AEGLISEEEIDIAVKRLFLARFRLGMFDPEEAVSYAQIPFGIVCSEAHNTLARQAAQKSM 397

Query: 383 VLLKNE-NILPLNKNKIKNVLVLGPNADKVHGLGGGSSEVPALYEITPLQGLKQKLGDNV 441
           VLLKN+ N+LPL+ +KIK + V+GPNAD V  L G    +P    +T L G+K K+G   
Sbjct: 398 VLLKNQKNLLPLSVDKIKRIAVIGPNADNVESLLGNYHGIPKK-PVTFLDGIKHKVGPKA 456

Query: 442 NITVMRARYDGV----LMPIASDYVTS---RHWTGTPAWNMVRYSDAARTQAIGDSAIVD 494
            +      +       L PI S Y  +   R       ++ +++      + + D   +D
Sbjct: 457 EVLYTEGVHPAEGFYNLKPIPSAYFETEDGRQGLKASYYDNLKWEGKPVLERVDDQ--ID 514

Query: 495 SAYSSPAGTTKEYVTMTAT-----IKPLKSGEHTLKTSVMGDFELKINGKTTVKHSST-- 547
            ++      +K+ +   +      + P  SG +          +++I+GK     S T  
Sbjct: 515 FSWEHQP-ISKDLIDNFSVKWEGYLVPPASGRYEFGVFSKRGMKIRIDGKEISNGSGTIH 573

Query: 548 SGDVVTQKIALNGGETYSFEILYSGNKNFTLG---WDAPGDLFTAEKEYIAAAKKADVVF 604
            G   T  ++L GG+ Y  E+ +  ++   +    W  P    +   E +A AK AD+  
Sbjct: 574 RGRYATDILSLEGGKKYKVEVTFFSDETNAIAQMLWAMPD--VSKIDEAVAMAKSADLAV 631

Query: 605 YFGGLTHGDDREAID----------RPHMKLPNHQDPVISKVLAANPNTVVFLIAGSAVE 654
              GL+   + E++D          R  + LP  Q+ ++  V       ++ L AGSA+ 
Sbjct: 632 VVLGLSQRLEGESMDVVTPGFDRGDRTAITLPAQQEALLKAVKETGKPVILVLNAGSAMA 691

Query: 655 MPWA-DKAKAIVWGWYGGMEAGNAYADMLFGDTNPSGKMPITLPKALEDTAPIALNDYNP 713
           + WA +   AI+   Y G E GNA AD++FGD NP+G++PIT  +++ED  P    DY+ 
Sbjct: 692 INWAKENVDAIISAGYPGEEGGNALADVVFGDYNPAGRLPITYYQSVEDLPPF--EDYDM 749

Query: 714 VESLYTEGVFIGYRWFEKQNIEPLFPFGHGLSYTQFKYNNIKLSSANIKGDQTVTVSATI 773
               Y        R+FE +   PL+PFG+GLSYT+F Y ++++  A +     V +S T+
Sbjct: 750 KGRTY--------RYFEGK---PLYPFGYGLSYTRFSYKDLEVP-AKVNAGDPVQISVTV 797

Query: 774 TNTGKVAGAEVVQLYLHDEQASVERPAKELKGFQKVFLKPGESKAVNITLNKRALSFWDE 833
           TN G  AG EVVQLYL+D++AS  RP ++L+GFQ++ LKPGESK VN TL+ R LS  + 
Sbjct: 798 TNIGSRAGDEVVQLYLNDKEASTMRPIRQLEGFQRIHLKPGESKVVNFTLSARQLSMING 857

Query: 834 NSNDWLAETGKFNVLLG 850
            S   + E G F++ +G
Sbjct: 858 ESKR-VIEEGVFSIHVG 873


Lambda     K      H
   0.316    0.132    0.389 

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: 1688
Number of extensions: 76
Number of successful extensions: 8
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: 866
Length of database: 906
Length adjustment: 43
Effective length of query: 823
Effective length of database: 863
Effective search space:   710249
Effective search space used:   710249
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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