Alignments for a candidate for bgl in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Pseudomonas putida KT2440

Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate PP_1403 PP_1403 periplasmic beta-D-glucoside glucohydrolase

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



>FitnessBrowser__Putida:PP_1403
          Length = 763

 Score =  946 bits (2444), Expect = 0.0
 Identities = 476/770 (61%), Positives = 602/770 (78%), Gaps = 12/770 (1%)

Query: 1   MKWLCSVGVAVSLAMQPALAENLFGNHPLTPEARD--AFVTDLLKKMTVDEKIGQLRLIS 58
           M  L  +G+A+ LA Q ALA       P  P  +D  AF+  L+ +MT  EKIGQLRLIS
Sbjct: 1   MMKLSLLGLAMGLASQAALAA------PTAPPLQDKQAFIEHLISQMTEAEKIGQLRLIS 54

Query: 59  VGPDNPKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRT 118
           +GP+ P++ IRE I  G++G  FN+ T  + R MQD  M  SRLKIP+FFAYD VHG+RT
Sbjct: 55  IGPEMPRDKIREEIAAGRIGGTFNSRTAPENRPMQDAAMR-SRLKIPMFFAYDTVHGERT 113

Query: 119 VFPISLGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDT 178
           +FPI LG+A++++++AV  VGR +A EA+ D L+MT+APMVD++RDPRWGR SEGFGEDT
Sbjct: 114 IFPIGLGMAATWDMEAVAKVGRTAAIEASADALDMTFAPMVDIARDPRWGRTSEGFGEDT 173

Query: 179 YLTSIMGETMVKAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMP 238
           YLTS +G+ MV++ QG SPA+  S+M  VKHFA YGAVEGG++YNTVDMS  +++NDY+P
Sbjct: 174 YLTSRIGQVMVRSFQGSSPANPDSIMAIVKHFALYGAVEGGRDYNTVDMSLPKMYNDYLP 233

Query: 239 PYKAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHG 298
           PY+A LDAG+G VMVALNS+NG PATS++WL+ D+LR EWGFKG+T+SDHGAI+ELI+HG
Sbjct: 234 PYRAALDAGAGGVMVALNSINGVPATSNTWLMNDLLRKEWGFKGVTISDHGAIQELIRHG 293

Query: 299 TAADPEDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGL 358
            A D  +A ++A+KAG+DMSM D  Y + LPGL+KSG+VT  ELD A R VL  KYDMGL
Sbjct: 294 VARDGREAAKLAIKAGIDMSMNDTLYGEELPGLLKSGEVTQRELDQAVREVLGAKYDMGL 353

Query: 359 FNDPYSHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGP 418
           F DPY  +G  E+D  D     RLHR+ AR+VAR S+VLL+NR +TLPLKK+GTIA+VGP
Sbjct: 354 FKDPYVRIGKAETDLKDYYGNDRLHREAARDVARRSLVLLENRNQTLPLKKAGTIALVGP 413

Query: 419 LADSQRDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDKGIVDFLN-LY 477
           LAD+  D+MGSW+A G    SVTV  G++ AV   AK++YAKG+N+T DK I D+LN L 
Sbjct: 414 LADAPIDMMGSWAADGKPVHSVTVREGLRRAVEGKAKLVYAKGSNVTGDKAIFDYLNFLN 473

Query: 478 EEAVKI--DPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLI 535
            +A +I  DPR P  +IDEA++AAKQ+DVVVAVVGES+GM+HE+SSRT + IP SQR+LI
Sbjct: 474 FDAPEIVDDPRPPAVLIDEAIKAAKQSDVVVAVVGESRGMSHESSSRTTLEIPASQRELI 533

Query: 536 TALKATGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKL 595
            ALKATGKPLVLVLMNGRPL++  E +QADAILETWFAGTEGGNAIADVLFGDYNPSGKL
Sbjct: 534 KALKATGKPLVLVLMNGRPLSISWEREQADAILETWFAGTEGGNAIADVLFGDYNPSGKL 593

Query: 596 PISFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSD 655
            I+FPRSVGQIP+YY+H   GRP+ P KP  YTS+YF+E NGPLYPFGYGLSY++F +S 
Sbjct: 594 AITFPRSVGQIPMYYNHTRIGRPFTPGKPGNYTSQYFEEPNGPLYPFGYGLSYSSFELSG 653

Query: 656 VTLSSPTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKP 715
           + LSS  ++R   + A V V NTGK  G TV+Q+YLQDV+ASMSRPVK+LK F+K+ L+P
Sbjct: 654 LNLSSKDLKRGDTLDAKVTVKNTGKVAGETVVQLYLQDVSASMSRPVKELKNFQKLMLEP 713

Query: 716 GERKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFELL 765
           GE +T++F I  + LKF+N Q++  AEPG+FNV +G+DS  V+Q SFELL
Sbjct: 714 GETRTLTFRISEDDLKFYNGQLQRVAEPGEFNVQVGLDSQAVQQQSFELL 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: 1545
Number of extensions: 51
Number of successful extensions: 3
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