Alignments for a candidate for bgl in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Sphingomonas koreensis DSMZ 15582

Align β-glucosidase (H1_GH3) (EC 3.2.1.21) (characterized)
to candidate Ga0059261_2310 Ga0059261_2310 Beta-glucosidase-related glycosidases

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



>FitnessBrowser__Korea:Ga0059261_2310
          Length = 762

 Score =  612 bits (1577), Expect = e-179
 Identities = 332/732 (45%), Positives = 456/732 (62%), Gaps = 22/732 (3%)

Query: 34  VDALLSEMTLDEKIGQLNQYTSRW---EMTGPAPQGKGE-QELLEMIRKGQVGSMLNVNG 89
           +DAL+++MTL EK GQL+   S W    +  PA       ++ +E +RKG +  + N +G
Sbjct: 42  IDALIAKMTLAEKAGQLSLMASAWGGSTVINPASGSNANFEQQVEEVRKGMLTGVFNGSG 101

Query: 90  AIATRNAQELAVKNSRLGIPLIFGYDVIHGYKTMFPIPLATAASWDPSAAELSARTAATE 149
               R  Q  A+K SRL IPLIF  D+IHG++T+FP+P+  AAS+DP+ AE +A  A+ E
Sbjct: 102 THMCRIMQTAAMKESRLKIPLIFAADIIHGHRTIFPVPVGEAASFDPALAERTAAAASYE 161

Query: 150 TAASGVHWTFAPMVDIARDARWGRIMEGAGEDPYLGAQMAAAQVKGFQGNDLSAENTIAA 209
            AA+G+ WTFAPMVD+ARD RWGR MEGAGED +LG   AAA+VKGFQG  L A +T+ A
Sbjct: 162 AAAAGIDWTFAPMVDVARDQRWGRTMEGAGEDVHLGNLFAAARVKGFQGASLKAIDTMMA 221

Query: 210 CAKHFAAYGFAEAGRDYNTVEITENTLRNVVLPPFKACADAGVATFMNAFNEIGGVTATA 269
           CAKHFAAYG AEAG DYNTV+++E TLR V  PPF+A   AG  + M++FNEI G+ +  
Sbjct: 222 CAKHFAAYGAAEAGLDYNTVDVSERTLREVYFPPFQAAFGAGALSAMSSFNEISGIPSNG 281

Query: 270 NKHLVRDILKGEWGFSGYVVSDWNSIGEIYEHGMTPDKKEAAFLAIKAGSDMDMEGNAYI 329
           N+ L+R +L+ EW + G+VVSD+    E+ +HG   D +EA  +A  AG DM M    Y 
Sbjct: 282 NEWLMRTVLRDEWKYQGFVVSDYTGDMEMIDHGFAADAREATKIAFMAGVDMSMTSGFYR 341

Query: 330 AHLKELVEEGRVDESMIDDAVRRILTLKFELGLFDDPFRYSDPGKEKI-LLSEEHLKAAR 388
            HL +LVE+G V  + +D++VR++L +K +LGLF+DPFR  D  +E     ++  L  +R
Sbjct: 342 DHLPDLVEKGEVPMARVDESVRKVLAIKAKLGLFEDPFRRIDEKREAARSRTKATLALSR 401

Query: 389 DVAKKSIVLLKNEKQLLPLKKSGQKIALIGDLADDKDSPLGSWRAQAVAGSAVSLLDGMK 448
           ++AKKSIVLLKNE  +LPL+K GQKIA+IG  A  +    G W        A+ L  G++
Sbjct: 402 EMAKKSIVLLKNEGDVLPLRKGGQKIAIIGPFAAGQHDLNGPWCVYGDNKLAIDLETGVR 461

Query: 449 NAIQDQRSLTFEQGPVFVTSTPQFTQHLQFNEKDLTGIDQAVELAEKSDVVVLALGENCF 508
           NA+     +T  +G       P              GI+ AV  A  +DVV+LA+GE+  
Sbjct: 462 NALGKNAQITVVEGSQVEAPLP-------------GGIEAAVAAARNADVVLLAIGESER 508

Query: 509 QTGEGRSQTEIGLKGVQQQLLEAVYAANKNMVVVLMNGRPLVIDWMAERVPAIVEAWHLG 568
            +GE +S+T I +   QQ L EAV A  K ++VVL NGR L ++   +  PAI+  W LG
Sbjct: 509 MSGEAQSRTSITVPAPQQALAEAVAATGKPVIVVLKNGRALALEGAVKNAPAILVTWFLG 568

Query: 569 SEAGNAIADVLFGDYNPSGKLPVSFPRSVGQCPIYYNHKNTGRP---IDTGTVFWSHYTD 625
           SE+GNAIADVLFGDY+PSG+LP+SFPR  GQ P YY+HK TGRP    D    + +HY  
Sbjct: 569 SESGNAIADVLFGDYSPSGRLPMSFPREPGQQPFYYSHKPTGRPNPSDDKLEEYKTHYRS 628

Query: 626 QSNEPLFPFGYGLSYTTFEYADLKLSSSEIRPGEKLKISVNLKNTGKLSGAEVVQLYIRD 685
             N  L+PFG+GL+Y   +YA+L      +    ++  +  + N G  +  EVVQLYIRD
Sbjct: 629 IPNSALYPFGHGLTYGKIDYANLTPDKGTLAWDGEIAFTATITNRGTRAAEEVVQLYIRD 688

Query: 686 LYGSVTRPVKELKGFKKISLNPGESRVVEFEISVRDLAFYTADGEWKAEPGHFHLWVGTN 745
              S+TRPV+ELK F+KI+L PG S  V F +    L F   D +   EPG F +W+  +
Sbjct: 689 RAASITRPVRELKAFRKIALAPGASETVRFVLKRAQLEFIGRDLKPTVEPGLFDVWIAPS 748

Query: 746 SN-EGLKGGFSL 756
           +  +G+   F+L
Sbjct: 749 AQAQGVHSTFTL 760


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: 1358
Number of extensions: 60
Number of successful extensions: 5
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: 762
Length adjustment: 40
Effective length of query: 718
Effective length of database: 722
Effective search space:   518396
Effective search space used:   518396
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 17 2021. 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