Alignments for a candidate for treC in Megamonas funiformis YIT 11815

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Megamonas funiformis YIT 11815

Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate WP_008539445.1 HMPREF9454_RS09460 alpha-glucosidase

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



>NCBI__GCF_000245775.1:WP_008539445.1
          Length = 556

 Score =  452 bits (1162), Expect = e-131
 Identities = 235/563 (41%), Positives = 330/563 (58%), Gaps = 23/563 (4%)

Query: 8   WWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSPQHDNGYD 67
           WW+K VVYQIYPKSF D+ G+G+GD+ GII KLDYL+ L V  +WL PIY SP  DNGYD
Sbjct: 6   WWQKTVVYQIYPKSFCDSNGDGIGDIPGIISKLDYLQDLGVGAIWLCPIYPSPLVDNGYD 65

Query: 68  IRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISSIDSPYRD 127
           I DY S+  EYGTMED ERL+SEA KR++K+VMDLV NHTS +HKWF E+ SS D+P RD
Sbjct: 66  ISDYCSVAKEYGTMEDMERLISEADKRNIKIVMDLVFNHTSDKHKWFEESRSSKDNPKRD 125

Query: 128 FYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEEVRKHVYD 187
           +YIW+  +E+GS PTNW S FGGSAW LDE + QYYLH F   Q DLNWEN+EVR+ ++D
Sbjct: 126 WYIWRDGKEDGSAPTNWRSIFGGSAWTLDEKTNQYYLHTFASAQPDLNWENKEVRQALFD 185

Query: 188 MMHFWFEKGIDGFRLDVINLISKDQRF--------PNAEEGDGRSFYTDGPRVHEFLHEM 239
             +FW +KG+ GFR+D I  I K   F         N       + Y DG  + +FLHE 
Sbjct: 186 AANFWLDKGVRGFRIDAIVYIKKPSEFKDLPVDGADNLASIAKATTYQDG--ILDFLHEF 243

Query: 240 NEKVFSHYDSMTVGEMSSTTVDHCIRYTNPDNKELDMTFSFHHLKVDYPNGEKW-ALAPF 298
            EKVF   D  TV E          ++   +N   DM+F F H+++ +     W     +
Sbjct: 244 REKVFDRADIFTVAEADGVYPSDFDKWIG-ENGAFDMSFDFSHIRLGFDEDCTWHKRKSW 302

Query: 299 DFLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDDGAYRVKSAKMLATAIHMM 358
             + +++  ++ +       GW  +++ NHD PR  + +   G     +AK +AT +  M
Sbjct: 303 KLIDIRKCFTEDEEAT-KDNGWVPVYFENHDLPRCTNYFFPQGTDTKLAAKFIATILLTM 361

Query: 359 QGTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGMADQDITAILQAKSRDNSR 418
           +GTP+IY+G+ELG+TN K+  I  Y D+ S+  Y    +  +  ++    +   SRDN+R
Sbjct: 362 RGTPFIYEGQELGVTNIKWPSIKMYNDISSIGQYELALKDKLTPKEAMKGVWKYSRDNAR 421

Query: 419 TPVQWDATENGGFTTGTPWIPVAGNYREINAEAALRDQNSVFYHYQKLIQIRKMYDIVTE 478
           +P+ W++    GFTTG PW+P+   Y ++N E    D+NSV  +Y+ LI++RK Y  + E
Sbjct: 422 SPMTWNSGSKAGFTTGRPWLPLNDEYPKLNVETETEDENSVLNYYKNLIKLRKQYPALIE 481

Query: 479 GTYEIIAKDDPNIFAYLR--HGSNEKLLVINNFYGTEAAFTLPDSLAPDEWKAEVLLTND 536
           G YE +    P I+AY R     +E+++VI N       + +P      E K   LL + 
Sbjct: 482 GDYEELLSYSPGIYAYARTTKDKSERIIVIANTTAKIRGYKIP------ELKGATLLAST 535

Query: 537 EAREGLQNMTLRPYESIVYRLTK 559
                 +   LR YE  VY++ K
Sbjct: 536 YGNR--EATLLRSYEVRVYKVKK 556


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: 1046
Number of extensions: 60
Number of successful extensions: 7
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: 556
Length adjustment: 36
Effective length of query: 525
Effective length of database: 520
Effective search space:   273000
Effective search space used:   273000
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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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