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

GapMind for catabolism of small carbon sources

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

Align Beta-glucosidase BoGH3A; Glycosyl hydrolase family protein 3A; BoGH3A; EC 3.2.1.21 (characterized)
to candidate WP_109737999.1 C1634_RS05265 glycosyl hydrolase

Query= SwissProt::A7LXS8
         (747 letters)



>NCBI__GCF_002899945.2:WP_109737999.1
          Length = 754

 Score =  804 bits (2076), Expect = 0.0
 Identities = 404/740 (54%), Positives = 516/740 (69%), Gaps = 28/740 (3%)

Query: 25  IAQDKEQTPVYLDDTQPIEVRVQDALNRMTVEEKTRLSYAQGKFSSPGCPRLGIPELWMS 84
           +AQ     P YLD+++P+E R+QDAL+RMT+EEK  + +AQ KFSSPG PRLGIPE W +
Sbjct: 19  MAQTNTTLPTYLDESKPVEQRIQDALSRMTLEEKVAMLHAQSKFSSPGVPRLGIPEFWTT 78

Query: 85  DGPHGVRAEINWNDWGYAGWTNDSCTAFPALTCLAASWNPLLAAKYGYAIGEEARYREKD 144
           DGPHGVR E+ W++W  AGWTNDS  A+PALT L+A+WN  ++  YG A+GEEARYR+KD
Sbjct: 79  DGPHGVRPEVMWDEWDQAGWTNDSIIAYPALTALSATWNKKMSWNYGKALGEEARYRKKD 138

Query: 145 VLLGPGVNIYRTPLNGRNFEYMGEDPYLASELCVPYIQGVQKNGVAACVKHYALNNQELW 204
           +LLGPGVNIYRTPLNGRNFEYMGEDPYL S++ VPYI+GVQ NGVA  VKH+ALNNQE++
Sbjct: 139 ILLGPGVNIYRTPLNGRNFEYMGEDPYLTSKMVVPYIKGVQSNGVATSVKHFALNNQEMF 198

Query: 205 RGHIDVQLSDRALYEIYLPAFKAAVERGKAWSIMGAYNKVRGTHATHHKLLNNDILKGEW 264
           R   +V + DR LYEIYLP FKAAV  G +W+IMGAY+  +G +A+ ++ L NDILK EW
Sbjct: 199 RHTSNVNVDDRTLYEIYLPPFKAAVTEGDSWTIMGAYDMYKGQYASQNQYLLNDILKKEW 258

Query: 265 NFDGCVITDWGAAHDTYEAAMYGLDIEMGSYTNGLTSESEFGYDDYYLGKSYLKMVREGK 324
           N+ G V++DWGA ++T +A   GLD+E GS+TNGL++ ++  YD+YYL K YL +++ GK
Sbjct: 259 NYKGVVVSDWGAVNNTEQAIHNGLDLEFGSWTNGLSAGTKNAYDNYYLAKPYLDLIKAGK 318

Query: 325 IPMEVVNDKAARVLRLIFRTAMNRRKPFGALTSEEHYRTAYEIATEGIVLLKNGTGKKQP 384
              + ++DK  R+LRL ++T MNR KPFG + SE+H   A EI  EGIVLLKN     Q 
Sbjct: 319 ADTKELDDKVTRLLRLAYKTTMNRNKPFGNIASEDHKAVAKEIGEEGIVLLKN-----QG 373

Query: 385 ALLPVPQGKYKRILVVGDNATRNLMLGGGSSELKVQKVISSLDGIKAKFGD--GVVYAQG 442
            +LP+   K K+I V+G+NA + + +GGGSS LKV+     LDGIK++FG    V YA+G
Sbjct: 374 NVLPIDINKAKKIAVIGENAIKIMTVGGGSSSLKVKYETLPLDGIKSRFGKQADVQYARG 433

Query: 443 YTSG-----RPMYGRADVIPQVTVDSLRNDAVEKAMNSDLVIFVGGLNKNHFQDCEGGDR 497
           Y          +    D+    +   L N+AVE A  SD VIFVGGLNK  FQD EG DR
Sbjct: 434 YVGDIGGEYNGVKSGQDLKDTRSEAELLNEAVELAKKSDYVIFVGGLNKADFQDSEGNDR 493

Query: 498 LSYELPFAQNELIEALLKVNKNLVAVIVSGNAVEMPWVKEIPSIVQSWYLGSVGGEALAD 557
            SY LP+ Q+ +I AL K NKNL  V+VSGNAV MPW+KE+P+++QSWYLGS  G ++A 
Sbjct: 494 KSYGLPYNQDHVISALAKANKNLAVVLVSGNAVAMPWIKEVPTVLQSWYLGSEAGNSIAS 553

Query: 558 VLSGEVTPSGKLPFSYPVKLEDCPAHFFGEISYPG--------------DSIRQEYKEDI 603
           VL+G+  PSGKLPF++PVKLED  AH  GE  YPG              + I   Y E +
Sbjct: 554 VLAGDANPSGKLPFTFPVKLEDNSAHQLGE--YPGQKDELAAGKGKDQKNPINITYNEGV 611

Query: 604 LVGYRWYDTKKVQPLFPFGYGMSYTTFEYSKPVISAQTMNTDGSIDVSVKVKNTGKVAGK 663
            VGYRW+DTK ++PLF FG+G+SYTTFE+ K      T++ DG I  ++ VKNTGK AG 
Sbjct: 612 FVGYRWHDTKNIKPLFSFGHGLSYTTFEFGKAKADQTTISQDGKITFTITVKNTGKKAGA 671

Query: 664 EIIQLYIGDEECSVLRPVKELKDFRKVQLLPNEEKEVKFTIKPEALQFFDDKQRTWVAEP 723
           E+ QLYI D + SV RP KELK F KV L P E+KEV FTI   AL +FD  +  WVAEP
Sbjct: 672 EVAQLYISDLKSSVPRPAKELKGFEKVYLNPGEQKEVAFTIDKTALSYFDAGKHDWVAEP 731

Query: 724 GKFKAYIAASSSDIRGTVTF 743
           G F+A I  SS  I+  V F
Sbjct: 732 GDFEALIGNSSDAIKTKVKF 751


Lambda     K      H
   0.318    0.136    0.411 

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: 1647
Number of extensions: 69
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: 747
Length of database: 754
Length adjustment: 40
Effective length of query: 707
Effective length of database: 714
Effective search space:   504798
Effective search space used:   504798
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: 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:

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 2024 update 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