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 (BglBX10;Fjoh_3392) (EC 3.2.1.21) (characterized)
to candidate Echvi_0398 Echvi_0398 Beta-glucosidase-related glycosidases

Query= CAZy::ABQ06406.1
         (814 letters)



>FitnessBrowser__Cola:Echvi_0398
          Length = 774

 Score =  814 bits (2103), Expect = 0.0
 Identities = 414/750 (55%), Positives = 536/750 (71%), Gaps = 20/750 (2%)

Query: 69  DLVKKMTEEEKANFLMGTGMPGFDGIK-PVVGAIEGRVPGAAGGTYEIKRLGIPAIIVAD 127
           +++  MT EEK+  LM TG    + +  P+ G  +  +    G TY    LGIP+I+++D
Sbjct: 40  EVIDAMTIEEKS--LMVTGAKRREVVPVPLPGRKQKNITAVGGYTYPFVHLGIPSIMLSD 97

Query: 128 GPAGLRIKPIRENDKNTYYCTAFPVGTALASTWNESLIEKVGKAMGNEVKEYGVDVLLAP 187
           GPAGLRI P R ND  TYYCTAFPVGT +AS+W+  L+EKVG AMG+E  EYGVD+LL+P
Sbjct: 98  GPAGLRIAPRRPNDPETYYCTAFPVGTLVASSWDPQLVEKVGNAMGHEALEYGVDILLSP 157

Query: 188 ALNIHRNPLCGRNFEYYSEDPLVSGKIASAMVKGIQLNGVGTSIKHFAANNQETNRLSIN 247
           A+NIHR+PL GR+FEYYSEDPL+SGK+ +A+V+GIQ  G+GT+IKHF ANNQETNR +I+
Sbjct: 158 AMNIHRDPLGGRSFEYYSEDPLISGKMGAALVRGIQSQGIGTAIKHFVANNQETNRRTID 217

Query: 248 EHISERAMREIYLKGFEITVKESNPWTVMSSYNLINGTYTSARKDLLTDILRNEWGFKGI 307
             +SERA+REIYL+GFEI VKE +PWTVMSSYN +NGTYT   ++LL  ILR EWGF G 
Sbjct: 218 AVVSERALREIYLRGFEIAVKEGDPWTVMSSYNKVNGTYTPQSEELLEIILRKEWGFDGF 277

Query: 308 VMTDWFGGFAGAQSIMAGSSNVTEQLSAGNDLLMPGIEAQKKAIIENINNKKLSKEVVDK 367
           V+TDW+GG            +  EQ+ AGNDLLMPG++    AI E + N  L KE+VD+
Sbjct: 278 VLTDWYGG-----------DDPVEQMKAGNDLLMPGLQDWSDAIAEALENGSLEKELVDR 326

Query: 368 NVERILELVLRSPIMENYKYSNKPNLKENAQITRQAASEGMILLKNDKNVLPFTNKKGKA 427
           N+ RIL+++ R+   ++Y YSNKPN KE+ +I R+AA E M+LLKND ++LP      K 
Sbjct: 327 NIARILDVITRTSTYKDYPYSNKPNFKESIKIAREAAGESMVLLKNDADILPLKPDIKKV 386

Query: 428 AVFGVTSYDFISGGTGSGDVNEAYTISLLDGLKNAGYSIDEELKTTYTPFVAKVKEAEME 487
           A FG  SY    GGTGSG VN  Y+ISL  GL+NAGY ID  L   YT ++ K K   +E
Sbjct: 387 APFGNYSYKLTVGGTGSGMVNNEYSISLAQGLENAGYEIDAALHEKYTDYLKKGKPQNLE 446

Query: 488 SRKKEGFLALPKR---LPELKLEKQEIAKHAASSELAIITIGRNSGEGGDRKVDNDFNLA 544
           +       A+PK    L EL L+   I ++A  S++A+++I R  GEGGDRK++  F L 
Sbjct: 447 ADSL--ITAMPKPDSILGELPLDASLIRQNAEESDIAMVSIMRVFGEGGDRKLET-FYLT 503

Query: 545 QDEVELINNVSEAFHSKGKKVVVILNIGGVIETASWKDKADAILLSWQPGQEGGNSVADV 604
           ++E  L+ NVSEAF +KGKKVVV+LNIGGVIETASW++ ADAILL+WQPGQEGGN++AD+
Sbjct: 504 EEEKNLLKNVSEAFRAKGKKVVVVLNIGGVIETASWRELADAILLAWQPGQEGGNAMADI 563

Query: 605 FSGKVNPSGKLTMTFPMKYEDTPSAKNWLGTPADNPANVTYEEGVYVGYRYYNTFNVKPS 664
            +GKVNPSGKL  TFP+ Y D P+ KN+ GTPA+NP  V +EEG+YVGYRYY++F V P+
Sbjct: 564 LTGKVNPSGKLATTFPLDYPDVPTTKNFPGTPAENPEKVVHEEGIYVGYRYYDSFAVNPA 623

Query: 665 YEFGFGNSYTTFNYSDVKLSSPVFNNAMTVSVTVKNTGKTAGKEVVQVYLSAPSKSIDKP 724
           YEFGFG SYT F+Y ++KL S  F N + V+  +KNTG  AG+EVVQ+YL+AP K++DKP
Sbjct: 624 YEFGFGLSYTDFSYDNLKLGSETFENEIEVTADIKNTGNKAGREVVQLYLAAPGKAMDKP 683

Query: 725 KEELKAFAKTKELKPGESETLQLVLSPKDLASFLENKNAWIAEAGTYKVLVGASSLDIKK 784
            +ELK FAKTK L PGES+T+  VL  + LASF+  ++AWIAEAG Y V VGASS DI+K
Sbjct: 684 VKELKNFAKTKLLAPGESQTITFVLDARSLASFVSERSAWIAEAGKYTVHVGASSRDIRK 743

Query: 785 TAEFTVSNEIVVEKVKKAFELDTPFKELKQ 814
           +A F +  E+ VEKV K         E K+
Sbjct: 744 SAGFDLEKELTVEKVHKVLVPQEKISEFKR 773


Lambda     K      H
   0.312    0.131    0.369 

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: 1720
Number of extensions: 85
Number of successful extensions: 4
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: 814
Length of database: 774
Length adjustment: 41
Effective length of query: 773
Effective length of database: 733
Effective search space:   566609
Effective search space used:   566609
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: 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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Candidates (tab-delimited)
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