Alignments for a candidate for tdcE in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcE in Bacteroides thetaiotaomicron VPI-5482

Align formate C-acetyltransferase (EC 2.3.1.54) (characterized)
to candidate 354264 BT4738 formate acetyltransferase (NCBI ptt file)

Query= BRENDA::P09373
         (760 letters)



>FitnessBrowser__Btheta:354264
          Length = 742

 Score =  823 bits (2127), Expect = 0.0
 Identities = 428/748 (57%), Positives = 526/748 (70%), Gaps = 14/748 (1%)

Query: 15  FTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDF 74
           F  G W +E+NVRDF+  N TPY GD SFL G TE T  +W++ +E +  E   +     
Sbjct: 7   FKDGLWSSEINVRDFVSHNITPYYGDASFLEGPTERTKAVWNRCLEALAEERENNGVRSL 66

Query: 75  DTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMI 134
           D    STITSH AGYI+K+ E IVGLQT+  LKRA+ PFGGI ++  +C     E+D  +
Sbjct: 67  DNVTVSTITSHKAGYIDKENELIVGLQTDELLKRAIKPFGGINVVSKACHENGVEVDDRV 126

Query: 135 KKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLM 194
           K IFT YRKTHN GVFDVYT +I   R  G LTGLPD Y RGRIIGDYRR+ALYGID L+
Sbjct: 127 KDIFTHYRKTHNDGVFDVYTEEIRSFRSLGFLTGLPDNYARGRIIGDYRRMALYGIDRLI 186

Query: 195 KDKLAQFTSLQADLEN--GVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNA 252
           + K       + DL N  G   +  IRLREE+AEQ +AL  MK M   YG D+S PA  A
Sbjct: 187 EAK-------KEDLHNLTGPMTDARIRLREEVAEQIKALKDMKVMGEYYGLDLSRPAYTA 239

Query: 253 QEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMK 312
           QEA+QW Y  YLAAVK Q+GAAMS G  S+FLD+Y+E +L  G ITE  AQE++D  V+K
Sbjct: 240 QEAVQWVYMAYLAAVKEQDGAAMSLGNVSSFLDIYLEYELSKGTITESFAQELIDQFVIK 299

Query: 313 LRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNM 372
           LRMVR LR   Y+++F+GDP W TES+GG   DGRT VTK SFRFL TLY +GPSPEPN+
Sbjct: 300 LRMVRHLRMQSYNDIFAGDPTWVTESLGGRLNDGRTKVTKTSFRFLQTLYNLGPSPEPNL 359

Query: 373 TILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQF 432
           T+LWS +LP  FK+F AKVSIDTSS+QYENDDLMR    +DDY IACCVS   +GKQ+QF
Sbjct: 360 TVLWSPELPEGFKEFCAKVSIDTSSIQYENDDLMREVRQSDDYGIACCVSYQEIGKQIQF 419

Query: 433 FGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYI 492
           FGAR NLAK +L AINGG  E     +      +  D L ++EVM+     +  +A+ Y 
Sbjct: 420 FGARCNLAKALLLAINGGRCENTGTVMVKNIPVLTSDTLKFEEVMDNYKKVLIEIARVYN 479

Query: 493 TALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDED 552
            A+NIIHYMHDKY YE + MAL D +    +A G+AGLS+A DSLSAIKYAKV   R++ 
Sbjct: 480 EAMNIIHYMHDKYYYEKAQMALVDTNPRINLAYGVAGLSIALDSLSAIKYAKVTARRNDI 539

Query: 553 GLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVV 612
           GL   F+IEGE+P FGN++ +VD L VDLV  F ++++KL  Y++A PT S+LTITSNV+
Sbjct: 540 GLTEGFDIEGEFPCFGNDNDKVDHLGVDLVYFFSEELKKLPVYKNARPTLSLLTITSNVM 599

Query: 613 YGKKTGNTPDGRRAGAPFGPGANPMHGRDQKGAVASLTSVAKLPFAYAKDGISYTFSIVP 672
           YGKKTG TPDGR  G  F PGANPMHGRD+ GA+ASL+SVAKL +  ++DGIS TFSIVP
Sbjct: 600 YGKKTGATPDGRAKGVAFAPGANPMHGRDKNGAIASLSSVAKLRYRDSQDGISNTFSIVP 659

Query: 673 NALGKDDEVRKTNLAGLMDGYFHHEASIEGGQHLNVNVMNREMLLDAMENPEKYPQLTIR 732
            +LG  DE R  NL  +MDGYF      +G  HLNVNV+NR+ML DAME+PE YPQLTIR
Sbjct: 660 KSLGATDEDRIENLVTMMDGYF-----TKGAHHLNVNVLNRDMLYDAMEHPENYPQLTIR 714

Query: 733 VSGYAVRFNSLTKEQQQDVITRTFTQSM 760
           VSGYAV F  L++E Q +VI+R+F + M
Sbjct: 715 VSGYAVNFVKLSREHQLEVISRSFHERM 742


Lambda     K      H
   0.318    0.135    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: 1364
Number of extensions: 55
Number of successful extensions: 3
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: 760
Length of database: 742
Length adjustment: 40
Effective length of query: 720
Effective length of database: 702
Effective search space:   505440
Effective search space used:   505440
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: 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