Alignments for a candidate for tdcE in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcE in Shewanella loihica PV-4

Align formate C-acetyltransferase (EC 2.3.1.54) (characterized)
to candidate 5209942 Shew_2390 formate acetyltransferase (RefSeq)

Query= BRENDA::P09373
         (760 letters)



>FitnessBrowser__PV4:5209942
          Length = 760

 Score = 1275 bits (3298), Expect = 0.0
 Identities = 616/760 (81%), Positives = 690/760 (90%)

Query: 1   MSELNEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVME 60
           M+E  E    AWEGFT GDW++EVNVRDFIQKNY PYEGDESFLAGATEAT+ LWDKVME
Sbjct: 1   MTEKTELFTKAWEGFTPGDWKSEVNVRDFIQKNYKPYEGDESFLAGATEATSALWDKVME 60

Query: 61  GVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIE 120
           G+K ENRTHAPVDFDT   STITSH AGYI++ LE IVGLQT+APLKRA++P GGI+M+E
Sbjct: 61  GIKQENRTHAPVDFDTDKVSTITSHAAGYIDQDLETIVGLQTDAPLKRAMLPNGGIRMVE 120

Query: 121 GSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIG 180
           GSC AY RELDP IK +++E RKTHNQGVFD+YTP+I+RCRKSGVLTGLPDAYGRGRIIG
Sbjct: 121 GSCAAYGRELDPNIKYVYSELRKTHNQGVFDIYTPEIMRCRKSGVLTGLPDAYGRGRIIG 180

Query: 181 DYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAK 240
           DYRR+ALYGIDYLM++K AQF+SLQA  E G +L  T++LREEIAEQH+ALGQMK+MAA 
Sbjct: 181 DYRRIALYGIDYLMQEKFAQFSSLQAQFEAGEDLSATMQLREEIAEQHKALGQMKQMAAS 240

Query: 241 YGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQ 300
           YG DISGPATNA+EAIQWTYFGYLAAVKSQNGAAMS GRTS+FLD+YIERD+  G +TEQ
Sbjct: 241 YGCDISGPATNAKEAIQWTYFGYLAAVKSQNGAAMSLGRTSSFLDIYIERDINNGVLTEQ 300

Query: 301 EAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNT 360
           +AQEMVDH VMKLRMVRFLRTPEYDELFSGDPIWATESI GMGLDGRTLVTK+SFRFL+T
Sbjct: 301 QAQEMVDHFVMKLRMVRFLRTPEYDELFSGDPIWATESIAGMGLDGRTLVTKSSFRFLHT 360

Query: 361 LYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACC 420
           LY MGPSPEPN+T+LWSEKLPLNFKK+ AKVSIDTSS+QYENDDLMRPDF++DDYAIACC
Sbjct: 361 LYNMGPSPEPNITVLWSEKLPLNFKKYCAKVSIDTSSIQYENDDLMRPDFDSDDYAIACC 420

Query: 421 VSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERM 480
           VSPM+VGK MQFFGARANLAKTMLYAINGGVDEKLK Q+GPK EPIK +VL++D+VM R+
Sbjct: 421 VSPMVVGKHMQFFGARANLAKTMLYAINGGVDEKLKTQIGPKFEPIKDEVLDFDDVMGRL 480

Query: 481 DHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAI 540
           D  M+WLA QY++ALN IHYMHDKYSYEA+LMALHDRDV RTMACGIAGLS+AADSLSAI
Sbjct: 481 DTMMEWLATQYVSALNAIHYMHDKYSYEAALMALHDRDVRRTMACGIAGLSIAADSLSAI 540

Query: 541 KYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIP 600
           K+AKVKPIRDE+G+A+DF+IEGEYP+FGNND RVDDLA +LVERFM KI+    YR+AIP
Sbjct: 541 KFAKVKPIRDENGIAVDFDIEGEYPKFGNNDARVDDLATELVERFMAKIRHKKMYRNAIP 600

Query: 601 TQSVLTITSNVVYGKKTGNTPDGRRAGAPFGPGANPMHGRDQKGAVASLTSVAKLPFAYA 660
           TQS+LTITSNVVYGKKTG TPDGR AGAPF PGANPMHGRD+KGA+ASLTSVAKLPFA+A
Sbjct: 601 TQSILTITSNVVYGKKTGTTPDGRPAGAPFAPGANPMHGRDEKGAIASLTSVAKLPFAHA 660

Query: 661 KDGISYTFSIVPNALGKDDEVRKTNLAGLMDGYFHHEASIEGGQHLNVNVMNREMLLDAM 720
           +DGISYTFSIVPNALGKDD+ R+ NLA LMDGYF H  + EGGQHLNVNVMNREML DA+
Sbjct: 661 QDGISYTFSIVPNALGKDDDGRRANLAALMDGYFAHNETREGGQHLNVNVMNREMLEDAV 720

Query: 721 ENPEKYPQLTIRVSGYAVRFNSLTKEQQQDVITRTFTQSM 760
            NP+KYPQLTIRVSGYAVRFN+LT EQQQDVITRTFT+ M
Sbjct: 721 VNPDKYPQLTIRVSGYAVRFNALTPEQQQDVITRTFTKGM 760


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: 1654
Number of extensions: 46
Number of successful extensions: 1
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: 760
Length adjustment: 40
Effective length of query: 720
Effective length of database: 720
Effective search space:   518400
Effective search space used:   518400
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