GapMind for catabolism of small carbon sources

 

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

Align beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate WP_066329731.1 BLR17_RS09380 family 1 glycosylhydrolase

Query= BRENDA::A4XIG7
         (453 letters)



>NCBI__GCF_900100165.1:WP_066329731.1
          Length = 465

 Score =  331 bits (848), Expect = 3e-95
 Identities = 191/465 (41%), Positives = 268/465 (57%), Gaps = 32/465 (6%)

Query: 5   KGFLWGAATASYQIEGAWNEDGKGESIWDRFTHQK--RNILYGHN--GDVACDHYHRFE- 59
           K FLWG A+A+YQ+EGA+  DGKGES WD  T++      + G    G+VA + Y R + 
Sbjct: 13  KPFLWGVASAAYQVEGAYQADGKGESKWDFLTNKVGVTQFIIGQKQTGNVAINMYDRTQY 72

Query: 60  -EDVSLMKELGLKAYRFSIAWTRIFPDGFGTVNQKGLEFYDRLINKLVENGIEPVVTLYH 118
            +D+ LMKELG+ +YRFS+ W+RI PDG G VN+K L  YD LI+ L   GIEPVVTLYH
Sbjct: 73  LKDIQLMKELGVNSYRFSLDWSRIIPDGIGAVNEKALAHYDVLIDDLKAAGIEPVVTLYH 132

Query: 119 WDLPQKLQDIGGWANPEIVNYYFDYAMLVINRYKDKVKKWITFNEPYCIAFLGYF----H 174
           +D P  L   GGW NPE++N+Y +YA +V  RY  KVK +ITFNEPY   F+  F     
Sbjct: 133 FDYPFALVQKGGWGNPEMINWYKNYAQIVFKRYGKKVKHFITFNEPYIEFFVAEFLMNME 192

Query: 175 GIHAPGIKDFKVAMDVVHSLMLSHFKVVKAVKENNIDVEVGITLNLTPVYLQTERLGYKV 234
               P +  F   M   H  +++  +V+K   + N+  ++G+T N +P            
Sbjct: 193 QSKEPAVTRFARGMMKAHRELVASAEVIKMYHKMNLGGKIGMTFNFSPCSPLDPN----- 247

Query: 235 SEIEREMVSLSSQLDNQLFLDPVLKGSYPQKLLDYLVQKD-----LLDSQKALSMQQEVK 289
           +  + +  +L  +L N +FLD   KG+YP++++D   + D       D  K L+  +   
Sbjct: 248 NPKDVQASALQEKLLNTVFLDGYFKGTYPKEVVDLFTKYDPAFQPAADDMKILAANK--- 304

Query: 290 ENFIFPDFLGINYYTRAVRLYDENSSWIFPIRW-EHPAGEYTEMGWEVFPQGLFDLLIWI 348
                PDFLGIN+Y  A+  YD +    F ++W +    +       V P+ L+  L+ I
Sbjct: 305 -----PDFLGINFYAPALVKYDPSEP--FEMKWMDINTDKIKSHNGPVRPEELYKFLVKI 357

Query: 349 KESYPQIPIYITENGAAY-NDIVTEDGKVHDSKRIEYLKQHFEAARKAIENGVDLRGYFV 407
           K+ Y    I ITENGA +  + +     V D  R +Y+K+H EA  KA + GV + GYF 
Sbjct: 358 KKEYNNPEIMITENGAGFEGEDIKATPIVKDPLRADYIKRHVEAVDKAKKEGVKMIGYFP 417

Query: 408 WSLMDNFEWAMGYTKRFGIIYVDYETQKRIKKDSFYFYQQYIKEN 452
           WS  DNFEW  GYTKRFG+IYVD+ETQ+RI K SFY YQ+ IK++
Sbjct: 418 WSGWDNFEWVFGYTKRFGLIYVDFETQERIPKQSFYEYQKIIKQH 462


Lambda     K      H
   0.322    0.140    0.439 

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: 705
Number of extensions: 38
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: 453
Length of database: 465
Length adjustment: 33
Effective length of query: 420
Effective length of database: 432
Effective search space:   181440
Effective search space used:   181440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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