Alignments for a candidate for treC in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Lactobacillus shenzhenensis LY-73

Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate WP_022529955.1 L248_RS09350 alpha-glucosidase

Query= CAZy::CAB12610.1
         (561 letters)



>NCBI__GCF_000469325.1:WP_022529955.1
          Length = 544

 Score =  546 bits (1407), Expect = e-160
 Identities = 278/557 (49%), Positives = 368/557 (66%), Gaps = 26/557 (4%)

Query: 8   WWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGYD 67
           WW++AVVYQIYP+SF D+ G+G+GDLNGI ++LDYL+ L VDVLWL+P+Y SP  DNGYD
Sbjct: 2   WWQEAVVYQIYPRSFQDSNGDGIGDLNGIRQRLDYLQRLGVDVLWLSPVYQSPNDDNGYD 61

Query: 68  IRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSPYRD 127
           I DY  I  ++GTM DF+ L++EAH R LK+VMDLVVNHTS EH+WF E+ SS ++PYRD
Sbjct: 62  ISDYERIMADFGTMADFDALLAEAHARGLKIVMDLVVNHTSDEHRWFAESRSSRNNPYRD 121

Query: 128 FYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVYD 187
           +YIW+ P  NG +P +WES F GSAW  DE + QYYLH+F   Q DLNW N  +R+ +Y 
Sbjct: 122 YYIWRDP-VNGGLPNDWESSFSGSAWSYDEGTQQYYLHMFSKKQPDLNWRNPAMRQDIYT 180

Query: 188 MMHFWFEKGIDGFRLDVINLISKDQRF--PNAEEGDGRSFYTDGPRVHEFLHEMNEKVFS 245
           MM +W +KGIDGFR+DVIN ISK + F  P A        +    +VH++L EMN++V S
Sbjct: 181 MMTWWLDKGIDGFRMDVINFISKPEDFSVPGA--------HGSQDQVHQYLEEMNQQVLS 232

Query: 246 HYDSMTVGEMSSTTVDHCIRYTNPDNKELDMTFSFHHLKVDY-PNGEKWALAPFDFLKLK 304
           HYD MTVGE    T +  +R+   D  EL+M F F H+ +D  P   +W    +    LK
Sbjct: 233 HYDIMTVGETPGVTPEGALRFAGFDTHELNMVFQFAHMGIDLDPEYGRWKPRAWHLSDLK 292

Query: 305 EILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDD-GAYRVKSAKMLATAIHMMQGTPY 363
            I+S WQT ++ G  WN+L+W NHDQPRVVSR+G+D   YRV+SAKML   +H  QGTPY
Sbjct: 293 AIMSRWQTALN-GQAWNSLYWNNHDQPRVVSRFGNDTPEYRVRSAKMLGAVLHYQQGTPY 351

Query: 364 IYQGEELGMTN-PKFTDISSYRDVESLNMYH--AFKEKGMADQDITAILQAKSRDNSRTP 420
           IYQGEELGMTN   FT ++ YRD+E+LN Y      ++ +   D+   +   SRDNSRTP
Sbjct: 352 IYQGEELGMTNAANFTSLADYRDIETLNAYQELVVDQEEITPADMLTAMHKNSRDNSRTP 411

Query: 421 VQWDATENGGFT-TG-TPWIPVAGNYREINAEAALRDQNSVFYHYQKLIQIRKMYDIVTE 478
           +QWD + N GFT TG TPWI +   Y EINA AAL D +SVFY YQ++ ++R+ Y I+T 
Sbjct: 412 MQWDDSANAGFTSTGVTPWIGLNDRYPEINAAAALADPDSVFYFYQEMNRLRREYPIITY 471

Query: 479 GTYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTLPDSLAPDEWKAEVLLTNDEA 538
           G Y ++A +D  ++ Y R    ++L +  NF  T+      ++ AP+  +       D+A
Sbjct: 472 GDYTLLAPEDEAVWTYERRDHGQRLCLTANF--TDQTVNRAEAAAPEGGRLLQSNYADDA 529

Query: 539 REGLQNMTLRPYESIVY 555
            E      LRPYE  VY
Sbjct: 530 GE-----ALRPYEVKVY 541


Lambda     K      H
   0.318    0.135    0.423 

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: 1134
Number of extensions: 55
Number of successful extensions: 9
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: 561
Length of database: 544
Length adjustment: 36
Effective length of query: 525
Effective length of database: 508
Effective search space:   266700
Effective search space used:   266700
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 (21.7 bits)
S2: 53 (25.0 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