Alignments for a candidate for bgl in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Stenotrophomonas chelatiphaga DSM 21508

Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate WP_057507620.1 ABB28_RS05205 1,4-beta-D-glucan glucohydrolase

Query= reanno::Korea:Ga0059261_1166
         (834 letters)



>NCBI__GCF_001431535.1:WP_057507620.1
          Length = 840

 Score =  875 bits (2260), Expect = 0.0
 Identities = 447/833 (53%), Positives = 572/833 (68%), Gaps = 20/833 (2%)

Query: 18  MLASLPVVMAATASARDDAAQAHPAMWPERRPTVPL--DPAVELRVADLLAKMSLEQKVG 75
           +  +L +     A A   A Q HP+ WP+  PT PL  DPA+E R+  L+A MS+E+KVG
Sbjct: 9   LCVALALACGTAAHAATPAGQIHPSQWPQ--PTWPLATDPAIERRIDALMATMSVEEKVG 66

Query: 76  QIIQADIASVTPADVHRYHLGSVLNGGNSDPGGRYNAPPRDWLAAADAFYAASMQPNGAL 135
           QI+Q DI S+TP +V +Y LGSVL GG SDPGGRYNA P +WLA ADA++ ASM  +G  
Sbjct: 67  QIVQGDIGSITPEEVKKYRLGSVLAGGGSDPGGRYNARPAEWLALADAYWEASMDTSGGG 126

Query: 136 PRIPVIWGSDAVHGHNNVVGATLFPHNIGLGAARNPDLIRRIGEATAIEMRVTGLDWTFA 195
             IP+IWG DA+HG +NVVGATLFPHNIGLGA RNP+L+R I   TA E R TG++WTFA
Sbjct: 127 HAIPIIWGIDAMHGQSNVVGATLFPHNIGLGATRNPELLREIARITAAETRTTGMEWTFA 186

Query: 196 PTLAVVRDDRWGRTYEGFGETPEIATAYAAPLIEGLQGKIGDKDWLRGPHIIATAKHFLG 255
           PT+AV +DDRWGR YEG+ E P +  +YA   +EGLQGK G  D+L   H++ T KHFLG
Sbjct: 187 PTVAVPQDDRWGRAYEGYSEDPALVASYAGVFVEGLQGKAGAADFLDDHHVMTTVKHFLG 246

Query: 256 DGGTRNGKDQGDTEIGEAGLRDLFSPPYLPALDAGVQSVMVSFSGWNGAKMHGNKSLLTG 315
           DGGT NGKDQGDT + EA LRD+ +  Y+PA+ AG QSVM SF+ ++G KMHG+K L+T 
Sbjct: 247 DGGTTNGKDQGDTTVSEAQLRDIHAAGYVPAIAAGAQSVMASFNSFHGEKMHGHKPLMTD 306

Query: 316 VVKQRWNFDGFLVGDWNGHGQVAGCTATNCPQSAIAGLDMYMAPDSWKALYEATLGQARD 375
           V+K R NF GF+VGDWNGHGQV GCT T+C Q+ IAG+DM MAPD+WK LYE+T+   +D
Sbjct: 307 VLKGRMNFGGFVVGDWNGHGQVKGCTNTDCAQTYIAGMDMAMAPDTWKGLYESTVKHVKD 366

Query: 376 GTLPIDRLDDAVRRILRVKIRAGLFEAGKPSSRPYAGRYELLGSAEHRALAREAVRQSLV 435
           GTLP+ RLDDAVRRIL  K+R GLFE  KPS+R   GR+ELLGS EHRA+AR+AVR+SLV
Sbjct: 367 GTLPMARLDDAVRRILLAKMRMGLFEKPKPSARALGGRFELLGSPEHRAVARQAVRESLV 426

Query: 436 LLKNANGLLPLKPGGRILVAGDGADNLTKQTGGWTLSWQGTGTQRSDFPNAQSIWEGIEA 495
           LLKN +GLLPL P  R+LVAGDGADN+TKQTGGWTL+WQG GT+R DFPNA ++W+G+++
Sbjct: 427 LLKNQDGLLPLSPKQRVLVAGDGADNMTKQTGGWTLTWQGDGTKREDFPNADTLWDGLKS 486

Query: 496 TVKAAGGTATLSVEGGYSAKPDAAIVVFGEEPYAEFQGDRPDVGYDDAKT--LALLRTLK 553
            V++AGG A L+V+G Y+ KPD AIVVFGE+PYAEFQGD PD+ +   ++  L L+R LK
Sbjct: 487 QVQSAGGKAELAVDGAYTRKPDVAIVVFGEDPYAEFQGDLPDLMFKGGRSGDLELIRKLK 546

Query: 554 TAGVPTVAVFLSGRAMWVNPFLNASDAFVAAWLPGSEGGGVADVLF------GKSDFSGK 607
             G+P VAVF+SGR +W+N  +NA+DAFVAAWLPGSEG GVADVL        + DFSGK
Sbjct: 547 ADGIPVVAVFISGRPLWLNREINAADAFVAAWLPGSEGAGVADVLLRGANGRPQHDFSGK 606

Query: 608 LGYSWPRSSDQTTVNIGDSNYDPLFPYGFGLKVADRGDLAALPETRA-TAAAAETGILFT 666
           L +SWPR +DQ   N+G   YDP F +G+GL  AD+G+L  L E        + T   F 
Sbjct: 607 LSFSWPRRADQYANNVGQPGYDPQFAFGYGLTYADKGNLPPLSEEPGIDPTKSRTSTWFD 666

Query: 667 AGKPGGGRRL-LLGRPGEL--AANPGPELIDARPADRSAQEDSLR--IRWTGAGQAVAAI 721
            G    G  L L G  GE     +P     D   A  +   D      ++T +G+ +  +
Sbjct: 667 RGVAATGLTLRLTGADGEAMDIVHPSATTPDGSLAMTAINTDVQEGGRQFTFSGKGLVEL 726

Query: 722 VQDVPVDLSRQANGDLALELELKVNAAPS-AEVSLLMRCGTDCAGGFPVRGILGEAAKTG 780
             + P+DL R+ NGD+ +   L+V+A P+ A VS L   G    G   +   L  +AK G
Sbjct: 727 RSNAPLDLDRETNGDVFVISTLRVDALPAGAPVSYLATSGKTTRGEVSIAQALA-SAKVG 785

Query: 781 KWTRVAVPLRCFEKAGVDMTRVETPLSIATAGSLDLTLSSARITSPSGPQLAC 833
           +WTRV VPLRC   AGVDM  VE P+++     + L+L+   I +    ++ C
Sbjct: 786 EWTRVGVPLRCLRIAGVDMKSVEIPMALQAGQGVRLSLAKVAIGTDYDQKVTC 838


Lambda     K      H
   0.317    0.135    0.412 

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: 2097
Number of extensions: 118
Number of successful extensions: 5
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: 834
Length of database: 840
Length adjustment: 42
Effective length of query: 792
Effective length of database: 798
Effective search space:   632016
Effective search space used:   632016
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: 56 (26.2 bits)

This GapMind analysis is from Sep 24 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