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_3261 Periplasmic beta-glucosidase (EC 3.2.1.21)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3261
          Length = 763

 Score =  962 bits (2488), Expect = 0.0
 Identities = 478/768 (62%), Positives = 602/768 (78%), Gaps = 8/768 (1%)

Query: 1   MKWLCSVGVAVSLAMQPALAENLFGNHPLTPEARDAFVTDLLKKMTVDEKIGQLRLISVG 60
           MK LC +G+ VSLA    LA       P   E +DAF++ L+K+MT+DEKIGQLRLIS+G
Sbjct: 1   MKKLCLLGLFVSLASHTVLAATT----PAPIENKDAFISHLMKQMTLDEKIGQLRLISIG 56

Query: 61  PDNPKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRTVF 120
           P+ P+E IR+ I  G +G  FN++TR + R MQD  M  SRLKIP+FFAYDV+HG RT+F
Sbjct: 57  PEMPREMIRKEIAAGNIGGTFNSITRAENRPMQDAAMR-SRLKIPMFFAYDVIHGHRTIF 115

Query: 121 PISLGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL 180
           PI L LASS+++DA+   GR++A EAA D L++T+APMVD+SRDPRWGR SEGFGEDTYL
Sbjct: 116 PIPLALASSWDMDAIGRSGRIAAKEAAADSLDITFAPMVDISRDPRWGRTSEGFGEDTYL 175

Query: 181 TSIMGETMVKAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMPPY 240
            S +   MVKA QG       S+M SVKHFA YGAVEGG++YN VDMS  +++ DY+PPY
Sbjct: 176 VSRIAGVMVKAFQGTGANAADSIMASVKHFALYGAVEGGRDYNVVDMSPVKMYQDYLPPY 235

Query: 241 KAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHGTA 300
           +A +DAG+G VMVALNS+NG PAT+++WL+ D+LR EWGFKG+ VSDHGAI ELIKHG A
Sbjct: 236 RAAIDAGAGGVMVALNSINGVPATANTWLMNDLLRKEWGFKGLAVSDHGAIFELIKHGVA 295

Query: 301 ADPEDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGLFN 360
           AD  +A ++A+KAG+DMSM D  Y K LPGL+K+G++   ++D+A R VL  KYDMGLF 
Sbjct: 296 ADGREAAKLAIKAGIDMSMNDTLYGKELPGLLKAGEIEQKDIDNAVREVLAAKYDMGLFK 355

Query: 361 DPYSHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGPLA 420
           DPY  +G  E DP DT AESRLHR EAR+VAR S+VLLKN+ ETLPLKK+  IA+VGPLA
Sbjct: 356 DPYLRIGKAEDDPADTYAESRLHRAEARDVARRSLVLLKNQGETLPLKKTAKIALVGPLA 415

Query: 421 DSQRDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDKGIVD---FLNLY 477
            +  D+MGSW+AAG   QSVT+  G+ +A+G  + ++YA+GANIT+DK I+D   FLN  
Sbjct: 416 KAPIDMMGSWAAAGRPEQSVTLFDGMTHALGAQSTLIYARGANITSDKKILDYLNFLNFD 475

Query: 478 EEAVKIDPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLITA 537
              V  DPR    +IDEAV+AA+QADVVVA VGES+GM+HE+SSRT++ IP +QR+LI A
Sbjct: 476 APEVVDDPRPANVLIDEAVKAAQQADVVVAAVGESRGMSHESSSRTDLNIPAAQRELIKA 535

Query: 538 LKATGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPI 597
           LKATGKPLVLVLMNGRPL++++E++QADAILETWF+GTEGGNAIADVLFGDYNPSGKLPI
Sbjct: 536 LKATGKPLVLVLMNGRPLSILEENEQADAILETWFSGTEGGNAIADVLFGDYNPSGKLPI 595

Query: 598 SFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSDVT 657
           + PRSVGQIP YY+HL+ GRP+ P KP  YTS+YF++  GPL+PFG+GLSYT F+++D+ 
Sbjct: 596 TVPRSVGQIPTYYNHLSIGRPFTPGKPGNYTSQYFEDTTGPLFPFGFGLSYTQFSLTDMA 655

Query: 658 LSSPTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKPGE 717
           LSS T+ + GK+ ASV V NTGKR+G TV+Q+Y+QDVT SM RPVK+LK F+K+ +K GE
Sbjct: 656 LSSTTLNKTGKLDASVVVKNTGKRDGETVVQLYIQDVTGSMIRPVKELKNFQKVLVKAGE 715

Query: 718 RKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFELL 765
           +K V F I  + LKF+N Q+KY AEPGKFNV IG+DS  V Q SFELL
Sbjct: 716 QKVVHFTITEDDLKFYNAQLKYAAEPGKFNVQIGLDSQDVTQQSFELL 763


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: 1574
Number of extensions: 66
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