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_066329580.1 BLR17_RS11760 glycosyl hydrolase

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



>NCBI__GCF_900100165.1:WP_066329580.1
          Length = 822

 Score = 1162 bits (3005), Expect = 0.0
 Identities = 572/816 (70%), Positives = 677/816 (82%), Gaps = 7/816 (0%)

Query: 5   IIKTARVSLLTALVISNLSWNSVSDDE--NNPPFLTVKGFTFRDLNKNGKLDIYEDTRLS 62
           I K  +VSL++ LV+S +SWN   D+   +  P +T+ GFTF DLN+NGKLDIYED RL+
Sbjct: 6   IRKVVKVSLVSTLVVSGISWNQKGDNNKIDKNPIITINGFTFTDLNRNGKLDIYEDYRLA 65

Query: 63  IHERAVDLVKKMTEEEKANFLMGTGMPGFD--GIKPVVGAIEGRVPGAAGGTYEIKRLGI 120
           + +R  DL+ KMT+EEKA+ L+G GMPGFD      + GA +G+VPG AGGTYEIKRLGI
Sbjct: 66  VEDRIQDLISKMTDEEKASMLIGIGMPGFDVNTFTFIPGADKGKVPGEAGGTYEIKRLGI 125

Query: 121 PAIIVADGPAGLRIKPIRENDKNTYYCTAFPVGTALASTWNESLIEKVGKAMGNEVKEYG 180
           PA+IV+DGPAGLRI P R+ND NTYY TAFPVGTALASTWNE LI  VGKAMGNEVKEYG
Sbjct: 126 PAVIVSDGPAGLRINPTRDNDTNTYYATAFPVGTALASTWNEELINNVGKAMGNEVKEYG 185

Query: 181 VDVLLAPALNIHRNPLCGRNFEYYSEDPLVSGKIASAMVKGIQLNGVGTSIKHFAANNQE 240
           VDVLL P +NIHRNPLCGRNFEYYSEDPL+SG IA+AMV G+Q NGVGTSIKHFAANNQE
Sbjct: 186 VDVLLGPGMNIHRNPLCGRNFEYYSEDPLLSGTIAAAMVNGVQSNGVGTSIKHFAANNQE 245

Query: 241 TNRLSINEHISERAMREIYLKGFEITVKESNPWTVMSSYNLINGTYTSARKDLLTDILRN 300
            NR+ IN HISERA+REIYL+GFEI VK + PWTVMSSYNL+NG YTSARKDLLT +LR 
Sbjct: 246 RNRMGINAHISERALREIYLRGFEIAVKTAQPWTVMSSYNLVNGEYTSARKDLLTTVLRE 305

Query: 301 EWGFKGIVMTDWFGGFAGAQSIMAGS--SNVTEQLSAGNDLLMPGIEAQKKAIIENINNK 358
           EWGFKG+VM+DWFGG+ G  +I +    S+V +QLSAGNDLLMPG+ +Q+ AI+ENI N 
Sbjct: 306 EWGFKGLVMSDWFGGYNGFGAISSKDAVSDVVKQLSAGNDLLMPGLPSQQNAILENIKNG 365

Query: 359 KLSKEVVDKNVERILELVLRSPIMENYKYSNKPNLKENAQITRQAASEGMILLKNDKNVL 418
           KL+ EV+D N+ RILELV+RSP+M NY+YSNKPNLKENA +TRQAA+EG ILLKND  VL
Sbjct: 366 KLTNEVIDTNLRRILELVMRSPVMNNYQYSNKPNLKENALVTRQAAAEGTILLKNDNAVL 425

Query: 419 PFTNKKGKAAVFGVTSYDFISGGTGSGDVNEAYTISLLDGLKNAGYSIDEELKTTYTPFV 478
           PF +K    AVFG TSYDFI+GGTGSGDVNEAY++SL+DGL N+G+SID++L+  Y P+V
Sbjct: 426 PFVSKSAPLAVFGNTSYDFIAGGTGSGDVNEAYSVSLIDGLTNSGFSIDKDLEDLYKPYV 485

Query: 479 AKVKEAEMESRKKEG-FLALPKRLPELKLEKQEIAKHAASSELAIITIGRNSGEGGDRKV 537
           A  K  EM  R+KEG  LA PKR+ EL L  + I   A +SELA+ITIGRN+GEG DRKV
Sbjct: 486 ADQKVKEMARREKEGGLLATPKRIIELDLNNETINNKAKTSELALITIGRNAGEGDDRKV 545

Query: 538 DNDFNLAQDEVELINNVSEAFHSKGKKVVVILNIGGVIETASWKDKADAILLSWQPGQEG 597
            +DFNLAQDE+ LIN+VSE FH++GKKVVV+LNIGGVIETASW+DK DAILL WQPGQEG
Sbjct: 546 ADDFNLAQDEINLINSVSEIFHAQGKKVVVVLNIGGVIETASWRDKVDAILLPWQPGQEG 605

Query: 598 GNSVADVFSGKVNPSGKLTMTFPMKYEDTPSAKNWLGTPADNPANVTYEEGVYVGYRYYN 657
           GNSV DVF+GKV PSGKLTMTFP+ YED  + KNW+GTPA+NP +V YEEG+YVGYRY+N
Sbjct: 606 GNSVVDVFTGKVTPSGKLTMTFPVNYEDAAATKNWIGTPAENPTSVNYEEGIYVGYRYFN 665

Query: 658 TFNVKPSYEFGFGNSYTTFNYSDVKLSSPVFNNAMTVSVTVKNTGKTAGKEVVQVYLSAP 717
           TFNVKPSYEFG+G SYTTF+YS++ LSS  FN+ M VSVT+ N GKTAGKEVV+++LSAP
Sbjct: 666 TFNVKPSYEFGYGLSYTTFDYSNLTLSSKTFNDKMIVSVTITNMGKTAGKEVVELFLSAP 725

Query: 718 SKSIDKPKEELKAFAKTKELKPGESETLQLVLSPKDLASFLENKNAWIAEAGTYKVLVGA 777
            KSIDKP+EELKAF KTK L+PGES+T+ L+L+ K+LASF+ NKNAWIAEAG YKVLVGA
Sbjct: 726 EKSIDKPREELKAFGKTKLLQPGESQTITLILNAKNLASFVPNKNAWIAEAGKYKVLVGA 785

Query: 778 SSLDIKKTAEFTVSNEIVVEKVKKAFELDTPFKELK 813
           SSL+IK+TAEFT+  E VVEK   AF LDTPF +LK
Sbjct: 786 SSLNIKETAEFTLEKEKVVEKTHAAFTLDTPFTDLK 821


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: 2014
Number of extensions: 91
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: 814
Length of database: 822
Length adjustment: 41
Effective length of query: 773
Effective length of database: 781
Effective search space:   603713
Effective search space used:   603713
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: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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