Alignments for a candidate for bgl in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Pseudomonas fluorescens FW300-N1B4

Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate Pf1N1B4_3419 Periplasmic beta-glucosidase (EC 3.2.1.21)

Query= CAZy::AAL21070.1
         (765 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3419
          Length = 763

 Score =  870 bits (2248), Expect = 0.0
 Identities = 427/735 (58%), Positives = 565/735 (76%), Gaps = 5/735 (0%)

Query: 33  ARDAFVTDLLKKMTVDEKIGQLRLISVGPDNPKEAIREMIKDGQVGAIFNTVTRQDIRQM 92
           +++AFV+DL+ +MT++EKIGQLRLI++      E IRE I  G++G  + +V+R   R M
Sbjct: 26  SKEAFVSDLINQMTLEEKIGQLRLIAIDEKMTPEKIREEIAAGRIGGTYGSVSRFVNRPM 85

Query: 93  QDQVMALSRLKIPLFFAYDVVHGQRTVFPISLGLASSFNLDAVRTVGRVSAYEAADDGLN 152
           QD     SRLKIP+FF +DV+HG RT+FPI L LASS+++ A+   GR++A EA+ DG++
Sbjct: 86  QDASQQ-SRLKIPMFFGWDVIHGHRTIFPIGLALASSWDIGAIELSGRIAAKEASADGID 144

Query: 153 MTWAPMVDVSRDPRWGRASEGFGEDTYLTSIMGETMVKAMQGKSPADRYSVMTSVKHFAA 212
           +T+APM+D++RDPRWGR SEGFGEDTYL S + + MV+A QG SP    S+M S KHFA 
Sbjct: 145 LTFAPMIDIARDPRWGRTSEGFGEDTYLVSRIAKAMVQAYQGASPNAPDSIMASAKHFAL 204

Query: 213 YGAVEGGKEYNTVDMSSQRLFNDYMPPYKAGLDAGSGAVMVALNSLNGTPATSDSWLLKD 272
           YGAVEGG++YN+VDM   R+  DY+PPY++ ++ G+GA+MVALNS+NG PA S++WL++D
Sbjct: 205 YGAVEGGRDYNSVDMGLARMHQDYLPPYRSAIEGGAGAMMVALNSINGVPAASNAWLMQD 264

Query: 273 VLRDEWGFKGITVSDHGAIKELIKHGTAADPEDAVRVALKAGVDMSMADEYYSKYLPGLI 332
           +LR  WGFKG+ +SDH  I +L++HG A +  +A R+A+KAGVDMSM D  Y   L GL+
Sbjct: 265 LLRKAWGFKGLVISDHNGINDLVQHGVAKNHREAARLAIKAGVDMSMNDFSYGPELQGLL 324

Query: 333 KSGKVTMAELDDATRHVLNVKYDMGLFNDPYSHLGPKESDPVDTNAESRLHRKEAREVAR 392
           +SG ++ + +D+A R VL  KYDMGLF DPY  +G    DP D NAE RLHR +AREVAR
Sbjct: 325 ESGAISQSNIDNAVREVLGAKYDMGLFEDPYRRIGIASEDPADNNAEHRLHRAQAREVAR 384

Query: 393 ESVVLLKNRLETLPLKKSGTIAVVGPLADSQRDVMGSWSAAGVANQSVTVLAGIQNAVGD 452
           +++VLLKN    LPLKK G IA++GPLA S  D+MGSWSA+GVA QSVT+  G++NA+  
Sbjct: 385 KTLVLLKNENGLLPLKKEGVIALIGPLAKSAVDIMGSWSASGVAEQSVTIYDGLKNAMTQ 444

Query: 453 GAKILYAKGANITNDKGIVDFLNLYEEAVKI--DPRSPQAMIDEAVQAAKQADVVVAVVG 510
           G+ ++YA+GAN+  D+ +V +L  Y+   KI  D R    MIDEAV+AA+QADVV+AVVG
Sbjct: 445 GS-LIYARGANLEEDQEVVKYLE-YQGVSKIENDARPAAEMIDEAVKAAQQADVVIAVVG 502

Query: 511 ESQGMAHEASSRTNITIPQSQRDLITALKATGKPLVLVLMNGRPLALVKEDQQADAILET 570
           E + M+HEA+SRT++ +P  Q +LITALKATGKPLVLVLMNGRPL++ KE +QADAILET
Sbjct: 503 EPRSMSHEAASRTSLDLPGRQSELITALKATGKPLVLVLMNGRPLSIGKEQKQADAILET 562

Query: 571 WFAGTEGGNAIADVLFGDYNPSGKLPISFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSR 630
           W++G+EGGNA+ADVLFGDYNPSGKLPI+FPRSVGQIP YYSHLNTGRPY       YTS+
Sbjct: 563 WYSGSEGGNAVADVLFGDYNPSGKLPITFPRSVGQIPNYYSHLNTGRPYIAGALRNYTSQ 622

Query: 631 YFDEANGPLYPFGYGLSYTTFTVSDVTLSSPTMQRDGKVTASVEVTNTGKREGATVIQMY 690
           YFD+++GPLYPFG+GLSYT F+++D+ LSS T+ +   + ASV V N G+R+G TV+Q+Y
Sbjct: 623 YFDQSHGPLYPFGFGLSYTDFSLTDMALSSTTLSKTDNLVASVMVKNIGQRDGETVVQLY 682

Query: 691 LQDVTASMSRPVKQLKGFEKITLKPGERKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFI 750
           ++DV  S+SRPVK+LK F+KI LK GE K V F I+   LKF+N Q++Y AEPG+F V I
Sbjct: 683 IRDVVGSVSRPVKELKNFQKIMLKAGEEKAVHFSINENDLKFFNSQLEYAAEPGEFRVQI 742

Query: 751 GVDSARVKQGSFELL 765
           G+DS  VK+ SFELL
Sbjct: 743 GLDSQDVKEQSFELL 757


Lambda     K      H
   0.316    0.132    0.380 

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: 1403
Number of extensions: 37
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: 765
Length of database: 763
Length adjustment: 40
Effective length of query: 725
Effective length of database: 723
Effective search space:   524175
Effective search space used:   524175
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 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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 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