Alignments for a candidate for bgl in Flavobacterium glycines Gm-149

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Flavobacterium glycines Gm-149

Align β-glucosidase (BglBX10;Fjoh_3392) (EC 3.2.1.21) (characterized)
to candidate WP_066329728.1 BLR17_RS09385 glycosyl hydrolase

Query= CAZy::ABQ06406.1
         (814 letters)



>NCBI__GCF_900100165.1:WP_066329728.1
          Length = 765

 Score =  755 bits (1949), Expect = 0.0
 Identities = 387/750 (51%), Positives = 519/750 (69%), Gaps = 41/750 (5%)

Query: 70  LVKKMTEEEKANFLMGTGM--PGFDG-----IKPVVGAIEGRVPGAAGGTYEIKRLGIPA 122
           +VK +T +EK   ++G GM  PG          P    I  +VPG +G T+ I RLGIP+
Sbjct: 35  VVKALTLDEKVKLVVGMGMHIPGASAGLLPPNDPEDDKITPKVPGTSGRTHAIDRLGIPS 94

Query: 123 IIVADGPAGLRIKPIRENDKNTYYCTAFPVGTALASTWNESLIEKVGKAMGNEVKEYGVD 182
           + ++DGPAG+    +        Y TA P+GT LASTW+  + +K G+ +G E K+YG+D
Sbjct: 95  LTLSDGPAGIHFMDLTAAKPK--YATAIPIGTLLASTWDTIMTKKAGEILGREAKDYGID 152

Query: 183 VLLAPALNIHRNPLCGRNFEYYSEDPLVSGKIASAMVKGIQLNGVGTSIKHFAANNQETN 242
           ++L PA NI RNPL GRNFEYYSEDP +SG IA+A+  GIQ  G+G S+KHFAANN ETN
Sbjct: 153 IVLTPAFNIQRNPLGGRNFEYYSEDPFLSGTIAAAVTNGIQKYGIGVSVKHFAANNTETN 212

Query: 243 RLSINEHISERAMREIYLKGFEITVKESNPWTVMSSYNLINGTYTSARKDLLTDILRNEW 302
           R+ +N  +SERA+REIYLKGFEI VK+SNPWT+M+SYNLINGTYTS  K+LLTDILR EW
Sbjct: 213 RMKLNTIVSERALREIYLKGFEIAVKKSNPWTLMTSYNLINGTYTSESKNLLTDILRKEW 272

Query: 303 GFKGIVMTDWFGGFAGAQSIMAGSSNVTEQLSAGNDLLMPGIEAQKKAIIENINNKKLSK 362
           GFKG+VM+DWF G            N    L AGNDL MPG   Q + II  + N  L+ 
Sbjct: 273 GFKGLVMSDWFAG-----------QNAATSLKAGNDLQMPGRPDQVQTIINAVKNGSLAM 321

Query: 363 EVVDKNVERILELVLRSPIMENYKYSNKPNLKENAQITRQAASEGMILLKNDKNVLPFTN 422
             +D++VER L LV+++    N  YSNKP+LK NA ++R  ASEGM+LLKND + LP  +
Sbjct: 322 SDLDESVERFLNLVVKTGTFNNVPYSNKPDLKGNAAVSRTVASEGMVLLKND-HALPL-S 379

Query: 423 KKGKAAVFGVTSYDFISGGTGSGDVNEAYTISLLDGLKNAGYSIDEELKTTYTPFVAKVK 482
           K    A+FG  SYD I+GGTGSGDV + YT+SL +GL N+G+ + +  K+ Y  ++    
Sbjct: 380 KSSTVALFGNASYDIIAGGTGSGDVVKKYTVSLDEGLVNSGFKLQQNNKSAYENYI---- 435

Query: 483 EAEMESRKKEGFLAL--PKRLPELKLEKQEIAKHAASSELAIITIGRNSGEGGDRKVDND 540
           ++E   +    F+ +  P  + E++++ + I   AA+S++AIITIGR SGE  DRKV +D
Sbjct: 436 KSEKAKKPAPSFMDVFNPFVIKEMEVKNEIITASAANSDVAIITIGRISGESKDRKVADD 495

Query: 541 FNLAQDEVELINNVSEAFHSKGKKVVVILNIGGVIETASWKDKADAILLSWQPGQEGGNS 600
           FNL   E + +  +SE+FH+K KKV+V++N GGVIETASW   ADAIL++WQPG EGGN+
Sbjct: 496 FNLTDAEKQTLKTLSESFHAKNKKVIVVINAGGVIETASWNQWADAILMAWQPGMEGGNA 555

Query: 601 VADVFSGKVNPSGKLTMTFPMKYEDTPSAKNWLG-------------TPADNPANVTYEE 647
           +AD+ SGKVNPSGKLT +FP+ Y D PS+KN+ G                  PA +TY++
Sbjct: 556 IADILSGKVNPSGKLTTSFPVSYIDVPSSKNFPGKQLPLKEGEILDPVMPTYPAEITYDD 615

Query: 648 GVYVGYRYYNTFNVKPSYEFGFGNSYTTFNYSDVKLSSPVFNNAMTVSVTVKNTGKTAGK 707
            +YVGYR++NT N+K +YEFGFG SYT F YSD+KLSS  F + +T ++T+KNTGKTAGK
Sbjct: 616 DIYVGYRHFNTNNIKTAYEFGFGLSYTQFEYSDIKLSSSEFKDKITATITIKNTGKTAGK 675

Query: 708 EVVQVYLSAPSKSIDKPKEELKAFAKTKELKPGESETLQLVLSPKDLASFLENKNAWIAE 767
           EVVQ+YL+APS  + KP EELK FAKTK L+ GES+T+   L+P +LAS+  N ++WIAE
Sbjct: 676 EVVQLYLNAPSVKLKKPSEELKGFAKTKLLQAGESQTISFTLTPGELASYDSNISSWIAE 735

Query: 768 AGTYKVLVGASSLDIKKTAEFTVSNEIVVE 797
           AG Y + +GASSL+IKKT +F ++ ++VV+
Sbjct: 736 AGNYTIQIGASSLNIKKTKQFHLAKDLVVK 765


Lambda     K      H
   0.312    0.131    0.369 

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: 1698
Number of extensions: 81
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: 814
Length of database: 765
Length adjustment: 41
Effective length of query: 773
Effective length of database: 724
Effective search space:   559652
Effective search space used:   559652
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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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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 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