Alignments for a candidate for bgl in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Herbaspirillum seropedicae SmR1

Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate HSERO_RS23930 HSERO_RS23930 beta-D-glucoside glucohydrolase

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



>FitnessBrowser__HerbieS:HSERO_RS23930
          Length = 784

 Score =  927 bits (2397), Expect = 0.0
 Identities = 465/765 (60%), Positives = 586/765 (76%), Gaps = 9/765 (1%)

Query: 4   LCSVGVAVSLAMQPALAENLFGNHPLTPEARDAFVTDLLKKMTVDEKIGQLRLISVGPDN 63
           LC++  +  L    A A+     +P     + AF+ DLL++MT++EKIGQLRLIS+GP+ 
Sbjct: 24  LCALACSAVLTGPTAHAQA----NPALLGDKTAFIDDLLRQMTLEEKIGQLRLISIGPEM 79

Query: 64  PKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRTVFPIS 123
           P + + E +  G+VG  FN+VTR + R +QD  M  SRLKIP+FFAYDV+HG RT FPI 
Sbjct: 80  PAKKLAEELAAGRVGGTFNSVTRPENRPLQDGAMR-SRLKIPMFFAYDVIHGHRTTFPIG 138

Query: 124 LGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYLTSI 183
           LGLASS+++D V    RVSA EAA D ++MT+APMVD+SRDPRWGR SEGFGED YL S 
Sbjct: 139 LGLASSWDMDVVARAMRVSAEEAAADSIDMTFAPMVDISRDPRWGRTSEGFGEDPYLVSR 198

Query: 184 MGETMVKAMQGKS-PADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMPPYKA 242
           + E  V+A+QG + P     VM SVKHFA YGAVEGG++YN V+M  QR++NDY+PPY+A
Sbjct: 199 IAEVSVRALQGDTKPIAANRVMASVKHFALYGAVEGGRDYNVVNMDPQRMYNDYLPPYRA 258

Query: 243 GLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHGTAAD 302
            +DAG+GAVMVALNS+NG PATS++WLL+D+LR +WGFKG+TVSDHGAI EL+ HG A +
Sbjct: 259 AIDAGAGAVMVALNSINGAPATSNTWLLQDLLRRDWGFKGLTVSDHGAITELVNHGVAQN 318

Query: 303 PEDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGLFNDP 362
             +A R+++KAG DMSMAD+ Y K LP L++SGKV+  ELD+A R +L  KYD+GLF DP
Sbjct: 319 DSEAARLSMKAGTDMSMADQVYIKQLPELVRSGKVSQQELDNAVRDILGAKYDLGLFKDP 378

Query: 363 YSHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGPLADS 422
           Y  +G    DP D  A+SRLHR++AREVA++S+VLL+NR   LPLKK+  IA+VGPLADS
Sbjct: 379 YVRIGRAADDPPDVYADSRLHRRDAREVAQQSMVLLENRNAALPLKKNARIALVGPLADS 438

Query: 423 QRDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDKGIVDFLNLY---EE 479
             D++GSWSAAG   Q++T+  G+Q A+G   K++YA+GANIT DK IVD+LN     + 
Sbjct: 439 HIDMLGSWSAAGKDKQTITLRQGLQAALGGQGKLVYARGANITEDKHIVDYLNFLNWDDP 498

Query: 480 AVKIDPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLITALK 539
            V  D RSP+AMIDEAV+AA+ ADV+VA VGES+GM+HE+SSRT++++PQSQ DL+ ALK
Sbjct: 499 EVVQDKRSPKAMIDEAVKAARHADVIVAAVGESRGMSHESSSRTSLSLPQSQLDLLKALK 558

Query: 540 ATGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPISF 599
           ATGKPLVLVLMNGRPL L    + A AILETW+ GTEGGNAIAD+LFGD NPSGKLPI+F
Sbjct: 559 ATGKPLVLVLMNGRPLDLNWARENASAILETWYTGTEGGNAIADILFGDVNPSGKLPITF 618

Query: 600 PRSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSDVTLS 659
           PRSVGQIP YY+H   GRPY   KP  YTS+YFDE NGPLYPFGYGLSYT F +S+V+LS
Sbjct: 619 PRSVGQIPSYYNHPRVGRPYTEGKPGNYTSQYFDEPNGPLYPFGYGLSYTEFKLSEVSLS 678

Query: 660 SPTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKPGERK 719
            P+M  DGKV ASV V N G+R GATV+Q+YL+DV AS+ RPVK+LK F K+ L+PGE K
Sbjct: 679 QPSMSADGKVEASVTVKNVGRRAGATVVQLYLRDVAASVVRPVKELKDFRKVMLQPGEEK 738

Query: 720 TVSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFEL 764
            V F ID +AL F+N +++Y AEPG+F V IG+DS  VK  SF L
Sbjct: 739 QVQFSIDRKALSFYNAKLEYVAEPGEFQVQIGLDSKEVKTASFNL 783


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: 1538
Number of extensions: 51
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: 784
Length adjustment: 41
Effective length of query: 724
Effective length of database: 743
Effective search space:   537932
Effective search space used:   537932
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