Alignments for a candidate for tdcE in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcE in Shewanella amazonensis SB2B

Align formate C-acetyltransferase (EC 2.3.1.54) (characterized)
to candidate 6937328 Sama_1498 formate C-acetyltransferase (RefSeq)

Query= BRENDA::P09373
         (760 letters)



>FitnessBrowser__SB2B:6937328
          Length = 760

 Score = 1266 bits (3275), Expect = 0.0
 Identities = 611/760 (80%), Positives = 683/760 (89%)

Query: 1   MSELNEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVME 60
           M++  E   TAWEGF  GDW+++VNVRDFIQ NYTPYEGD+SFLAG T AT  LW KVME
Sbjct: 1   MTDKTELFQTAWEGFVPGDWKSDVNVRDFIQTNYTPYEGDDSFLAGPTAATNALWAKVME 60

Query: 61  GVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIE 120
           G+K ENRTHAP+DFDT   STITSHDAGYI K+LE IVGLQT+APLKRA++P GGI+M+E
Sbjct: 61  GIKEENRTHAPLDFDTDKVSTITSHDAGYIEKELETIVGLQTDAPLKRAMLPNGGIRMVE 120

Query: 121 GSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIG 180
            SC AYNREL+  IK +++E RKTHNQGVFD+YTP+IL CRKSGVLTGLPDAYGRGRIIG
Sbjct: 121 SSCAAYNRELNADIKYVYSELRKTHNQGVFDIYTPEILACRKSGVLTGLPDAYGRGRIIG 180

Query: 181 DYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAK 240
           DYRRVALYGIDYLM DKL QFTSLQ+  E G +L+ T++LREEIAEQHRAL QMK+MAAK
Sbjct: 181 DYRRVALYGIDYLMADKLKQFTSLQSRFEEGEDLQATMQLREEIAEQHRALAQMKKMAAK 240

Query: 241 YGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQ 300
           YGYDISGPA NAQEAIQWTYFGYLAAVKSQNGAAMS GRTS+F+D+YIERDLK G +TE+
Sbjct: 241 YGYDISGPAKNAQEAIQWTYFGYLAAVKSQNGAAMSLGRTSSFIDIYIERDLKNGTLTEE 300

Query: 301 EAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNT 360
           +AQEM+DH VMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTK+SFRFL+T
Sbjct: 301 QAQEMIDHFVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKSSFRFLHT 360

Query: 361 LYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACC 420
           LY MGPSPEPN+T+LWSEKLP NFK F AKVSIDTSS+QYENDDLMRPDF +DDYAIACC
Sbjct: 361 LYNMGPSPEPNITVLWSEKLPENFKTFCAKVSIDTSSIQYENDDLMRPDFESDDYAIACC 420

Query: 421 VSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERM 480
           VSPM+VGK MQFFGARANLAKTMLYAINGGVDEKLK+Q+GPKSEPI  + L+YD+VM R+
Sbjct: 421 VSPMVVGKHMQFFGARANLAKTMLYAINGGVDEKLKVQIGPKSEPITSEYLDYDDVMSRL 480

Query: 481 DHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAI 540
           D+ M+WLA QY++ALN IH+MHDKYSYEA+LMALHDRDV RTMACGIAGLS+AADSLSAI
Sbjct: 481 DNLMEWLATQYVSALNAIHFMHDKYSYEAALMALHDRDVRRTMACGIAGLSIAADSLSAI 540

Query: 541 KYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIP 600
           KYAKVKP+RDE G+A+DFEIEG+YP+FGNND RVDD+A  LVE FM KI+    YR+AIP
Sbjct: 541 KYAKVKPVRDEHGIAVDFEIEGDYPKFGNNDARVDDIACMLVEGFMAKIRNKKMYRNAIP 600

Query: 601 TQSVLTITSNVVYGKKTGNTPDGRRAGAPFGPGANPMHGRDQKGAVASLTSVAKLPFAYA 660
           TQS+LTITSNVVYGKKTGNTPDGRRAGAPF PGANPMHGRD+KGA+ASLTSVAKLPFA+A
Sbjct: 601 TQSILTITSNVVYGKKTGNTPDGRRAGAPFAPGANPMHGRDEKGAIASLTSVAKLPFAHA 660

Query: 661 KDGISYTFSIVPNALGKDDEVRKTNLAGLMDGYFHHEASIEGGQHLNVNVMNREMLLDAM 720
           +DGISYTFSIVPNALGKD++ R+ NLA LMDGYF H    EGGQHLNVNVMNREML DA+
Sbjct: 661 QDGISYTFSIVPNALGKDEKARERNLAALMDGYFRHSEGREGGQHLNVNVMNREMLEDAI 720

Query: 721 ENPEKYPQLTIRVSGYAVRFNSLTKEQQQDVITRTFTQSM 760
            NP+KYPQLTIRVSGYAVRFNSLT EQQQDVITRTFTQ +
Sbjct: 721 ANPDKYPQLTIRVSGYAVRFNSLTPEQQQDVITRTFTQGL 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: 1648
Number of extensions: 55
Number of successful extensions: 2
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