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 coniferin β-glucosidase (Cbg1;Cbg-1) (EC 3.2.1.21|3.2.1.126) (characterized)
to candidate Ga0059261_0769 Ga0059261_0769 Beta-glucosidase-related glycosidases

Query= CAZy::AAA22082.1
         (818 letters)



>FitnessBrowser__Korea:Ga0059261_0769
          Length = 838

 Score =  531 bits (1369), Expect = e-155
 Identities = 312/822 (37%), Positives = 448/822 (54%), Gaps = 35/822 (4%)

Query: 2   IDDILDKMTLEEQVSLLSGADFWTTVAIERLGVPKIKVTDGPNGARGGGSLVGGVKSACF 61
           + D++ ++TL+E++ LL+G        I RLG+P +K+TDGP G R       G  +  F
Sbjct: 37  VADLMARLTLDEKILLLAGESSMALNPIPRLGIPAVKMTDGPTGVRSPD----GKPATVF 92

Query: 62  PVAIALGATWDPELIERAGVALGGQAKSKGASVLLAPTVNIHRSGLNGRNFECYSEDPAL 121
           PV +AL A+W+P+L    G A+  + K+ GA VLLAPTVNI R+   GRNFE YSEDP L
Sbjct: 93  PVGVALAASWNPDLAATVGAAVARETKAHGADVLLAPTVNIVRTPRWGRNFETYSEDPWL 152

Query: 122 TAACAVAYINGVQSQGVAATIKHFVANESEIERQTMSSDVDERTLREIYLPPFEEAVKKA 181
           +    + Y+ GVQ +G+  ++KHF  N  E  R  + S VD+RTL EIYLP FE  V++A
Sbjct: 153 SGRMGLGYVRGVQGEGIGVSLKHFAVNNQESYRFVVDSIVDQRTLHEIYLPAFEMVVREA 212

Query: 182 GVKAVMSSYNKLNGTYTSENPWLLTKVLREEWGFDGVVMSDWFGSHSTAETINAGLDLEM 241
              +VM+SYNK+NGTY +EN WLLT +L++EWG+ G V+SDW  +H+TAE +NAG+DLEM
Sbjct: 213 DPWSVMASYNKINGTYAAENRWLLTDLLKKEWGYRGFVVSDWGATHTTAEAVNAGMDLEM 272

Query: 242 PGPWRDRGEKLVAAVREGKVKAETVRASARRILLLLERVGAFEKAPDLAEHALDLPEDRA 301
           PGP +  G+KL AAV EGKV    +  +ARR++ L+ R G  E+     E A  L +  A
Sbjct: 273 PGPPKHFGDKLKAAVAEGKVSTAQIDDNARRMVRLIVRSGVIERGASRPEAATPLRQS-A 331

Query: 302 LIRQLGAEGAVLLKNDGVLPLAKSSFDQIAVIGPNAASARVMGGGSARIAAHYTVSPLEG 361
           + R+   E  VLLKN+GVLP  + S   +AVIGPNA   R+ GGGS+ +    T +PL+ 
Sbjct: 332 IARKAAEEAMVLLKNNGVLPFDR-SIRSLAVIGPNADVVRMQGGGSSNVVPFETQTPLDA 390

Query: 362 IRAALSNANSLRHAVGCNNNRL-----IDVFSGE-------MTVEYFKGRGFESRPVHVE 409
           +RAAL     + +  G +N          +FS +       +T  YF        PV  E
Sbjct: 391 LRAALPGVR-ITYEKGVDNEETPPAADAKLFSPDGKRGETGLTGSYFMTADASGEPVKTE 449

Query: 410 TVEKGEFFWFDLPSGDLDLADFSARMTATFVPQETGEHIFGMTNAGLARLFVDGELVVDG 469
            V +   +     +G       + R    F P+  G H F +   G  R+ +DG+++++ 
Sbjct: 450 RVTRFVRWISGNVAGPKATGYAAIRWDGMFWPRTGGVHEFSVRGTGTPRVTLDGKVILEK 509

Query: 470 YDGWT-KGENFFGTANSEQRRAVTLGAARRYRVVVEYEAPKASLDGINICALRFGVEKPL 528
                    +  G     +   VTL A R Y + ++Y     +  G     L FGV +P 
Sbjct: 510 ASKVVPDNRDVLGFPVPRRTVQVTLEAGRGYPIRIDY-----ANGGTPYENLSFGVREP- 563

Query: 529 GDAGIAEAVETARKSDIVLLLVGREGEWDTEGLDLPDMRLPGRQEELIEAVAETNPNVVV 588
                  AV  A+ +D  +++VG     + EG D  ++ LPG Q  L+EA+A  NP   V
Sbjct: 564 -QPSFDAAVAAAKGADAAIVIVGSSSTTEGEGYDRANIDLPGEQNRLVEAIAAANPKTAV 622

Query: 589 VLQTGGPIEMPWLGKVRAVLQMWYPGQELGNALADVLFGDVEPAGRLPQTFPKALTDNSA 648
           V+  G  + MPW  K  A++ MW PG+    ALADVL G V P+G+LP TFP+   D+ A
Sbjct: 623 VVNAGAAMTMPWHEKAPAIVSMWLPGEGGAAALADVLTGKVNPSGKLPVTFPQRSGDDLA 682

Query: 649 ITDDPSIYPGQDGHVRYAEGIFVGYRHHDTREIEPLFPFGFGLGYTRFTWGAPQLSGTEM 708
                     +     Y+EG+ VGYR +  R ++PLFPFG GL YT F +    +     
Sbjct: 683 DL--------KTSKSAYSEGLLVGYRGYQARGVKPLFPFGHGLSYTSFAYSPLNVPARAS 734

Query: 709 GADGLTVTVDVTNIGDRAGSDVVQLYVHSPNARVERPFKELRAFAKLKLAPGATGTAVLK 768
           GA  +TV + V N G R G +VVQLYV         P + LRAF K+ +  G      L 
Sbjct: 735 GAKPVTVKLTVRNTGKRTGQEVVQLYVEPVEPMAGDPPRTLRAFQKVAIPAGGKREVTLT 794

Query: 769 IAPRDLAYFDVEAGRFRADAGKYELIVAASAIDIRASVSIHL 810
           + PR  +++DV+AG +R   G Y ++  +S+ DIR +  I +
Sbjct: 795 LDPRAFSFYDVKAGGWRVRPGAYRVLAGSSSEDIRQAGEIRV 836


Lambda     K      H
   0.318    0.136    0.402 

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: 1679
Number of extensions: 80
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: 818
Length of database: 838
Length adjustment: 42
Effective length of query: 776
Effective length of database: 796
Effective search space:   617696
Effective search space used:   617696
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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Protein sequences (fasta format)
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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