GapMind for catabolism of small carbon sources

 

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

Align β-glucosidase (Bgl;Fbgl;FmBGL) (EC 3.2.1.21) (characterized)
to candidate WP_109739238.1 C1634_RS23580 beta-glucosidase BglX

Query= CAZy::AAB66561.1
         (726 letters)



>NCBI__GCF_002899945.2:WP_109739238.1
          Length = 775

 Score = 1140 bits (2948), Expect = 0.0
 Identities = 559/727 (76%), Positives = 633/727 (87%), Gaps = 1/727 (0%)

Query: 1   MTLDEKIGQLNLPSSGDFTTGQAQSSDIGKKIEQGLVGGLFNIKGVNKIKAVQKVAIEKS 60
           MTLDEKIGQLNLPSSGDFTTG A+SSDIGKK+EQGLVGGLFNIKG  KI+AVQKVA+E S
Sbjct: 49  MTLDEKIGQLNLPSSGDFTTGLAKSSDIGKKVEQGLVGGLFNIKGAEKIRAVQKVAVENS 108

Query: 61  RLKIPMIFGMDVIHGYETTFPIPLGLASSWDMDLIQRSAQIAAKEASADGINWTFSPMVD 120
           RLKIP+IFGMDVIHGYETTFPIPLGLA+SWDM+L+Q+SA++AAKEAS+DGINWTFSPMVD
Sbjct: 109 RLKIPLIFGMDVIHGYETTFPIPLGLAASWDMNLVQQSARVAAKEASSDGINWTFSPMVD 168

Query: 121 VSREPRWGRVSEGSGEDPYLGSEIAKAMVYGYQGKDLSLKNTILACVKHFALYGAPEGGR 180
           +SREPRWGRVSEGSGEDPYLGSEIAK MVYGYQGKDL+    ILACVKHFALYGA E GR
Sbjct: 169 ISREPRWGRVSEGSGEDPYLGSEIAKNMVYGYQGKDLANGTNILACVKHFALYGAGESGR 228

Query: 181 DYNTVDMSHIRMFNEYFPPYKAAVDAGVGSVMASFNEVDGVPATGNKWLMDDVLRKQWGF 240
           DYNTVDMSH+RMFNEYFPPYKAAVDAGV SVMASFNEVDGVPATG++WL  +VLR +W F
Sbjct: 229 DYNTVDMSHVRMFNEYFPPYKAAVDAGVASVMASFNEVDGVPATGSRWLQTEVLRNKWNF 288

Query: 241 NGFIVTDYTGINEMIQHGMGDLQQVSALALNAGVDMDMVGEGFLTTLKKSLSEGKVTEQQ 300
            GF+VTDYTGINEM+ HGMGDLQQVSALAL AGVDMDMVGEGFLTTLKKSLSEGKVT+ +
Sbjct: 289 KGFVVTDYTGINEMVDHGMGDLQQVSALALKAGVDMDMVGEGFLTTLKKSLSEGKVTQAE 348

Query: 301 ITLAARRILEAKYDLGLFDDPYRYTDEKRAKAEVFSKPHREEARNIAAQSMVLLKNDKQT 360
           I LAA+R+LE+KYDLGLF DPY+Y D K A  EV+S  +R  ARN+AAQSMVL+KN+ Q 
Sbjct: 349 IDLAAKRVLESKYDLGLFTDPYKYGDAKLAAKEVYSMENRNIARNVAAQSMVLMKNENQV 408

Query: 361 LPLKAGGTVAVIGPLANNNENMTGTWSVASRMKDAVSIMTGLKETV-KGVNFIYAKGSNV 419
           LPLK  GTVAVIGPL NN+ NM GTWSVA++   AV++M GL+ +  K V F+ AKG+N+
Sbjct: 409 LPLKKSGTVAVIGPLVNNSLNMAGTWSVAAKHDKAVNLMQGLQASYGKEVKFLSAKGANI 468

Query: 420 FYDAKMEEKATMFGKTANRDSRSKEELLKEAVATANKADVVVLAIGETAELSGESSSRAN 479
            YDAK+E+     GK  +RD+RSKEELLKEAV  ANKADV+VLAIGE+AE+SGESSSR  
Sbjct: 469 DYDAKLEDIYAAHGKKTDRDNRSKEELLKEAVDVANKADVIVLAIGESAEMSGESSSRTE 528

Query: 480 IEIPQAQKDLLTELKKTGKPIVMVLFTGRPLVLNDENKQADAIVNAWFAGSEAGYAIADV 539
           I IPQ+Q DLL ELKKTGKPI MVLFTGRPL L +     D+I+NAWFAGSEAG AIADV
Sbjct: 529 ITIPQSQVDLLNELKKTGKPIAMVLFTGRPLALTNVKDTPDSILNAWFAGSEAGNAIADV 588

Query: 540 LYGKVNPSGKLPMTFPRSVGQVPIYYNAKNTGRPLSDERSDKCEFEKFRSNYIDECNTPL 599
           L+GKVNPSGKLPMTFPRS+GQVPIYYNAKNTGRPLS E +DKCE+++FRSNY+DECNTPL
Sbjct: 589 LFGKVNPSGKLPMTFPRSLGQVPIYYNAKNTGRPLSQELTDKCEYQRFRSNYMDECNTPL 648

Query: 600 FPFGYGLSYTTFNYSDIQLNKTQLSGNDQLTASVTLTNNGKYDGNEVVQLYIRDMVGSVT 659
           +PFG+GLSYT F YSDI ++ T   GN  + ASVT+TN+G YDG EVVQLYIRDMVGS+T
Sbjct: 649 YPFGFGLSYTKFGYSDIAVSNTSPKGNQTIQASVTVTNDGNYDGAEVVQLYIRDMVGSIT 708

Query: 660 RPVKELKGFQKVFLKAGESKIVTFNITPEDLKFYNSALKYDWEPGEFDIMIGTNSHDVKH 719
           RPVKELKGFQKVFLK GES+ VTF+ITPE LKFYN  LKYDWE G+FD+MIGT+S DVKH
Sbjct: 709 RPVKELKGFQKVFLKKGESRKVTFDITPETLKFYNGDLKYDWESGDFDVMIGTSSADVKH 768

Query: 720 AKINWNK 726
           +KINW K
Sbjct: 769 SKINWTK 775


Lambda     K      H
   0.315    0.133    0.383 

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: 1734
Number of extensions: 51
Number of successful extensions: 2
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: 726
Length of database: 775
Length adjustment: 40
Effective length of query: 686
Effective length of database: 735
Effective search space:   504210
Effective search space used:   504210
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 (21.5 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:

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:

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:

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:

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