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 (SalA) (EC 3.2.1.21) (characterized)
to candidate Ga0059261_3889 Ga0059261_3889 Beta-glucosidase-related glycosidases

Query= CAZy::AAF21798.1
         (732 letters)



>FitnessBrowser__Korea:Ga0059261_3889
          Length = 748

 Score =  699 bits (1804), Expect = 0.0
 Identities = 390/732 (53%), Positives = 477/732 (65%), Gaps = 28/732 (3%)

Query: 9   AALATSLCLTAFAGGAMAQAKGAWQNTSLSPDERARLLDAELTLDERISLLHGPMPLPFP 68
           AAL T+  L AF       A+ A    +     RA  + A +TLDE+I+L+HG  P P  
Sbjct: 6   AALLTASALAAFTA-TQGVAQQAPVPAATDARVRAESIVARMTLDEKIALVHGLFP-PLT 63

Query: 69  GSPPIPEGPSLVPVI--FPGVPRLGIPALKETDASLGVTNPMNVRPGDTATALPSGLALA 126
              P+ E   LVP      G PRLG+P ++E+DASLGV N +  R GD ATALPS LA A
Sbjct: 64  KVKPVNE---LVPSAGHIEGNPRLGVPLVRESDASLGVANQVEQRKGDVATALPSSLATA 120

Query: 127 STFNPKLSYDGGAAIAKEAASKGFNVLLAGGANLARDPRNGRNFEYLGEDPLLAGILAGE 186
           +TF+P+++  GGA I  EA +K FNVLLAGG NL RDP  GRNFEYLGEDPLLAG LAG 
Sbjct: 121 ATFDPEIARAGGAMIGAEARAKRFNVLLAGGVNLNRDPWGGRNFEYLGEDPLLAGELAGA 180

Query: 187 SIRGIQSQNIISTVKHFSLNGQETNRHWGNSVIDEAAHRESDLLAFQIAIERGQPGSVMC 246
            I G+QS  I+ST+KHF+LN QET R   ++ I EAA RESDLLAFQIAIE+G+P SVMC
Sbjct: 181 HIAGVQSNRIVSTIKHFALNSQETGRMVLDARIGEAALRESDLLAFQIAIEKGKPASVMC 240

Query: 247 AYNLVNGAYSCGNDHLLNKVLKGDWGYKGWVMSDWGAVPATDFALK-GLDQQSGQQLDEK 305
           AYN VNG ++C ND LLN+VLK DWG+ GWVMSDWG V +T+ A K GLDQQSGQ+LD  
Sbjct: 241 AYNKVNGDWACENDFLLNQVLKRDWGFSGWVMSDWGGVHSTEKAAKAGLDQQSGQELDRA 300

Query: 306 IWFGDLLKEAAAAGTIPAERLSDMSRRILRSMFAAGFFDG--KPGKPVVDLDAHAAIAKQ 363
           ++F   LKEA   G +P  RL DM  R L  +  +G +D          D  A+A +A++
Sbjct: 301 MYFDAPLKEAVENGRVPMARLDDMVVRYLTGLIESGAYDTPMPATAQTPDYAANALVAQR 360

Query: 364 VADEGIVLLANDKGLLPLAAGSQKIAVIGGFADQGVLSGAGSSQVTSVGGNPVVIPVGGE 423
            A+ GIVLL N  G+LPLAA ++KI VIGG AD GVLSG GSSQV SVGG P+ IP+   
Sbjct: 361 AAEAGIVLLKNQGGILPLAATAKKIVVIGGGADVGVLSGGGSSQVRSVGGAPIEIPL-AH 419

Query: 424 GMLAAFLRQAYHNSSPLKALKERLPNATIRFNDGRYSAAAAALARQSDIVILFANQWMSE 483
           G  A+F+R  YH SSPL+AL++ LP A +RF DGR   A    A+ +D+ I+FA QW +E
Sbjct: 420 GPAASFVRVTYHASSPLEALRKALPGAQVRFVDGRNLNATVDAAKAADLAIVFATQWTTE 479

Query: 484 GMDAYDLKLPQGQDALIEAVAEANPNAVIVLQTGGPVLMPWKDKVGAIVSAWYSGQKGGE 543
             D  DL+L   QDALI AVA A P  V VL TGGPV MPW D+V A+V AWY GQ+GGE
Sbjct: 480 AEDVPDLRLQNHQDALIAAVAAAQPKTVAVLTTGGPVTMPWLDRVPAVVQAWYPGQRGGE 539

Query: 544 AIADILVGKTNPSGRLPSTFPASADQYPHPEVPGWNL-----------------PEKQQF 586
           AIA+IL GK NPSGRLP TFPA   Q P P+  G +                   E + F
Sbjct: 540 AIANILTGKVNPSGRLPITFPAHEGQAPRPQPVGLDTFTALQAAAAANPANPGGYELKSF 599

Query: 587 DVVYEEGSDVGYRRFAAKGMKPLFPFGHGLSYTTFAYDKLKVKGGETLEVSFQVTNTGKL 646
            V Y EGSDVGYR +  +G KPLF FGHGLSYT+FAY K  V GG+ L V+F VTNTGK 
Sbjct: 600 PVDYVEGSDVGYRWYEKQGHKPLFAFGHGLSYTSFAYGKAAVTGGKRLTVAFDVTNTGKR 659

Query: 647 QGKDAPQIYLAGANGQKLQRLIGFEKIDLKPGERRTVTIKADPRLLARFDEQGHQWRIDG 706
            G D PQ+Y+         RL  F++I+L+PGE R VT+ A+PR+LA +D     WRI G
Sbjct: 660 AGADVPQVYVTREGSNIPMRLAAFKRIELQPGETRRVTLTAEPRILADYDTSLPGWRIRG 719

Query: 707 GDYDVVVGRSAT 718
           G Y + + R AT
Sbjct: 720 GTYRIAIARDAT 731


Lambda     K      H
   0.316    0.135    0.401 

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: 1488
Number of extensions: 79
Number of successful extensions: 6
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: 732
Length of database: 748
Length adjustment: 40
Effective length of query: 692
Effective length of database: 708
Effective search space:   489936
Effective search space used:   489936
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.

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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