GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgl in Chryseobacterium viscerum 687B-08

Align β-glucosidase (H1_GH3) (EC 3.2.1.21) (characterized)
to candidate WP_103233888.1 C1634_RS08970 beta-glucosidase BglX

Query= CAZy::AEW47970.1
         (758 letters)



>NCBI__GCF_002899945.2:WP_103233888.1
          Length = 740

 Score =  704 bits (1818), Expect = 0.0
 Identities = 360/722 (49%), Positives = 490/722 (67%), Gaps = 21/722 (2%)

Query: 30  IRTKVDALLSEMTLDEKIGQLNQYTSRWEMTGPAPQGKGEQELLEMIRKGQVGSMLNVNG 89
           I  KV  LLS+MTL+EK+GQ+ QY+     TGP  Q      +LE I+KG+VGSMLNV G
Sbjct: 23  IDQKVAELLSKMTLEEKVGQMVQYSGFEYATGP--QQSNSAVVLEEIKKGKVGSMLNVAG 80

Query: 90  AIATRNAQELAVKNSRLGIPLIFGYDVIHGYKTMFPIPLATAASWDPSAAELSARTAATE 149
           +  T+  Q+LA++ SR+ IPL+FG DVIHGY+T FP+ L  AASWD    E S R AATE
Sbjct: 81  SEETKAFQKLAMQ-SRMKIPLLFGQDVIHGYRTTFPVNLGQAASWDLGMIEKSERIAATE 139

Query: 150 TAASGVHWTFAPMVDIARDARWGRIMEGAGEDPYLGAQMAAAQVKGFQGNDLSAENTIAA 209
            +A G+HWTFAPMVDIARD RWGR+MEG+GED YLG ++  A++KGFQG  L + + + A
Sbjct: 140 ASAYGIHWTFAPMVDIARDPRWGRVMEGSGEDTYLGTKIGLARIKGFQGRGLGSLDAVMA 199

Query: 210 CAKHFAAYGFAEAGRDYNTVEITENTLRNVVLPPFKACADAGVATFMNAFNEIGGVTATA 269
           CAKHFAAYG A  GRDYN+V+++   L    LPPFKA A+AGVATFMN+FN+I G+ ATA
Sbjct: 200 CAKHFAAYGAAVGGRDYNSVDMSLRQLNETYLPPFKAAAEAGVATFMNSFNDINGIPATA 259

Query: 270 NKHLVRDILKGEWGFSGYVVSDWNSIGEIYEHGMTPDKKEAAFLAIKAGSDMDMEGNAYI 329
           N+++ R++LKG+W +  +VVSDW SIGE+  HG   D  EAA  AI+ GSDMDME   Y+
Sbjct: 260 NQYIQRNLLKGKWNYKDFVVSDWGSIGEMIPHGYAKDASEAAEKAIQGGSDMDMESRVYM 319

Query: 330 AHLKELVEEGRVDESMIDDAVRRILTLKFELGLFDDPFRYSDPGKEKILL-SEEHLKAAR 388
           A L +LV+EG+VD  ++DDA  RILT KFE+GLFDDP+R+S   ++K    ++E+ K  R
Sbjct: 320 AELPKLVKEGKVDPKLVDDATARILTKKFEMGLFDDPYRFSSEKRQKEQTDNQENRKFGR 379

Query: 389 DVAKKSIVLLKNEKQLLPLKKSGQKIALIGDLADDKDSPLGSWRAQAVAGS--AVSLLDG 446
           +   KSIVLLKN+  +LPL K+ + +ALIG    +  +  G W       +   VS  DG
Sbjct: 380 EFGSKSIVLLKNQGNILPLSKTTKTVALIGPFGKETVANHGFWSIAFKDDNQRIVSQFDG 439

Query: 447 MKNAIQDQRSLTFEQGPVFVTSTPQFTQHLQFNEKDLTGIDQAVELAEKSDVVVLALGEN 506
           +KN +    +L + +G                +++D T   +A+E A+K+DVV++ LGE 
Sbjct: 440 IKNQLDKNSTLLYAKG-------------CNVDDQDKTQFAEAIETAKKADVVIMTLGEG 486

Query: 507 CFQTGEGRSQTEIGLKGVQQQLLEAVYAANKNMVVVLMNGRPLVIDWMAERVPAIVEAWH 566
              +GE +S++ IG  GVQ+ LL+ +    K +++++  GRPL+ +W ++ +P I   W 
Sbjct: 487 HAMSGEAKSRSNIGFTGVQEDLLKEIAKTGKPIILMINAGRPLIFNWASDNIPTIAYTWW 546

Query: 567 LGSEAGNAIADVLFGDYNPSGKLPVSFPRSVGQCPIYYNHKNTGRPI--DTGTVFWSHYT 624
           LG+EAGN+IADVLFG  NP GKLP+SFPR+ GQ P+YYNH NTGRP   +T   + S Y 
Sbjct: 547 LGTEAGNSIADVLFGTVNPGGKLPMSFPRTEGQIPVYYNHYNTGRPAKNNTDRNYVSAYI 606

Query: 625 DQSNEPLFPFGYGLSYTTFEYADLKLSSSEIRPGEKLKISVNLKNTGKLSGAEVVQLYIR 684
           D  N+P +PFGYGLSYT F+Y+D+ L+S+ +   + L ISV + NTGK  G EVVQLYIR
Sbjct: 607 DLDNDPKYPFGYGLSYTDFKYSDMVLNSASLTGNQTLNISVTVSNTGKYDGEEVVQLYIR 666

Query: 685 DLYGSVTRPVKELKGFKKISLNPGESRVVEFEISVRDLAFYTADGEWKAEPGHFHLWVGT 744
           DL+G V RPVKELKGF+K+ +  GES+ VEF+++  DL F+  D  +  E G F + +GT
Sbjct: 667 DLFGKVVRPVKELKGFQKVWIKKGESKKVEFKLTPEDLKFFDDDLNFDWEGGEFDIMIGT 726

Query: 745 NS 746
           +S
Sbjct: 727 DS 728


Lambda     K      H
   0.317    0.134    0.392 

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: 1474
Number of extensions: 60
Number of successful extensions: 7
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: 740
Length adjustment: 40
Effective length of query: 718
Effective length of database: 700
Effective search space:   502600
Effective search space used:   502600
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 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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