Alignments for a candidate for lacZ in Bacteroides clarus YIT 12056

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Bacteroides clarus YIT 12056

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate WP_009122666.1 BUB52_RS03815 beta-glucosidase

Query= SwissProt::E7CY69
         (757 letters)



>NCBI__GCF_900129655.1:WP_009122666.1
          Length = 803

 Score =  249 bits (637), Expect = 3e-70
 Identities = 207/686 (30%), Positives = 313/686 (45%), Gaps = 93/686 (13%)

Query: 36  GIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNPELIHKVGEAMAE 95
           GIP     +G HGL  +               AT  P    + S+WN EL+ + G    +
Sbjct: 144 GIPVDFTNEGIHGLNHT--------------KATPLPAPIAIGSTWNKELVRRAGVIAGQ 189

Query: 96  ECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGVQSKGVGTSLKHF 155
           E        +  P +++ R+P  GR  E + E+P+L       +V G+QS+GV  +LKH+
Sbjct: 190 EAKALGYTNVYAPILDVVRDPRWGRTLECYGEEPFLIAALGTEMVNGIQSQGVAATLKHY 249

Query: 156 AA----NNQETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRINGVHSAQN 211
           A             R D  ++PR L E++   F+ +++ + P  +M SYN  +GV  + +
Sbjct: 250 AVYSVPKGGRDGHCRTDPHVAPRELHELFLYPFKKVIQNSHPMGVMSSYNDWDGVPVSAS 309

Query: 212 HWLLTDVLRDEWGFDGIVMSDWGA--------------DHDRGASLNAGLNLE---MPPS 254
           ++ LT++LR+E+GFDG V+SD  A              D      L AGLN+     PPS
Sbjct: 310 YYFLTELLREEYGFDGYVVSDSQAVEFVESKHHVADTYDEAVRQVLEAGLNVRTHFTPPS 369

Query: 255 ---------YTDDQIVYAVRDGLITPAQLDRMAQGMID--LVNKTRAAMSIDNYRFDVDA 303
                      + +I  A  D  ++     +   G+ D   V  T AA ++     ++D 
Sbjct: 370 DFILPIRRLLEEKKISMATIDKRVSEVLRVKFRLGLFDRPYVTDTGAADNVGGADRNMDF 429

Query: 304 HDEVAHQAAIESIVMLKNDDAILPLNAGPVANPSATPQKIAVIGEFA-----RTPRYQGG 358
             E+  QA    +V+LKN++ ILPL+   +       +K+ V G  A      T RY   
Sbjct: 430 VKEMQQQA----LVLLKNENNILPLDKQRI-------KKVLVTGPLADEDNFMTSRYGPN 478

Query: 359 GSSHITP-TKMTSFLDTLAERGIKADFAPGFTLDLEPADPALE--------------SEA 403
           G   +T    + ++L  +AE     D+A G  + ++   PA E              +EA
Sbjct: 479 GLETVTVLAGLRAYLQGVAE----VDYAKGCDI-VDAGWPATEILPVPMNEREKRGIAEA 533

Query: 404 VETAKNADVVLMFLGLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVI 463
           V  A  +DVV+  LG  E    E   R +LD+P +Q  LLE + A  + V++VL NG  +
Sbjct: 534 VAKAGESDVVIAVLGEDEYRTGESRSRTSLDLPGRQQQLLEALHATGKPVILVLINGQPL 593

Query: 464 TVAPWAK-NAKGILESWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSMLNWPG 522
           TV  WA      ILESW  G  GG  +A+ +FG+ +P GKL  + P  +      LN+P 
Sbjct: 594 TV-NWANAYIPAILESWFPGCQGGTVIAETLFGEHNPGGKLTVTFPKSVGQ--IELNFPF 650

Query: 523 EEG-HVDYGEGVFAGYRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGANTA---TVT 578
           + G H    +    G       G+   YPFG+GLSY TF  + + V+     T    TV 
Sbjct: 651 KPGSHGSQPKSGPNGSGATRVIGEL--YPFGFGLSYTTFAYSDLEVSPLRQRTQGEYTVK 708

Query: 579 ATVTNTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAY 638
             VTNT      E VQ+YV    + V     +L+GF +  LK GE++ V   L       
Sbjct: 709 VNVTNTGKRAGDEVVQLYVRDKVSSVITYDSQLRGFERVSLKPGETRQVTFSLKPEDLQI 768

Query: 639 WSEKYNDWHVEAGEYAIEVGVSSRDI 664
                N W VE GE+ + +G SS+DI
Sbjct: 769 LDRNMN-WTVEPGEFEVMIGASSQDI 793


Lambda     K      H
   0.315    0.132    0.393 

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: 1355
Number of extensions: 69
Number of successful extensions: 8
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: 757
Length of database: 803
Length adjustment: 41
Effective length of query: 716
Effective length of database: 762
Effective search space:   545592
Effective search space used:   545592
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: 42 (22.0 bits)
S2: 55 (25.8 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)
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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 2024 update 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