Alignments for a candidate for SST in Methanosarcina barkeri Fusaro

GapMind for Amino acid biosynthesis

Alignments for a candidate for SST in Methanosarcina barkeri Fusaro

Align Serine O-succinyltransferase; SST; EC 2.3.1.- (characterized)
to candidate WP_011307393.1 MBAR_RS12890 homoserine O-acetyltransferase

Query= SwissProt::A0A1D3PCM3
         (517 letters)



>NCBI__GCF_000195895.1:WP_011307393.1
          Length = 579

 Score =  218 bits (555), Expect = 5e-61
 Identities = 144/435 (33%), Positives = 209/435 (48%), Gaps = 44/435 (10%)

Query: 109 LDWGGLLPEFDIAYETWGQLNEKKDNVILLHTGLSASSHAHSTEA-NPKPGWWEKFIGPG 167
           L+ G  L    I YE +G++N  K NVIL+   L+  +HA      + KPGWW   IGP 
Sbjct: 38  LESGKTLSHVRIEYEMYGKMNADKSNVILVCHALTGDAHAAGFHTGDKKPGWWNIVIGPN 97

Query: 168 KTLDTDKYFVICTNVLGGCYGSTGPSTVDPSDGKKYATRFPILTIEDMVRAQFRLLDHLG 227
           K  DT++Y ++C+N++GGC GSTGPS+++P  GK Y   FPILTI DMV AQ +L++HLG
Sbjct: 98  KAFDTERYCIVCSNIIGGCKGSTGPSSINPETGKPYGISFPILTIADMVNAQKKLVEHLG 157

Query: 228 VRKLYASVGSSMGGMQSLAAGVLFPERVGKIVSISGCARSHPYSIAMRHTQRQVLMMDPN 287
           V++L+A  G SMGGMQ L   V +PE V K ++I+  A + P  IA     R+ +  DP 
Sbjct: 158 VKQLFAVAGGSMGGMQVLQWTVSYPEMVKKAIAIATTASTTPQQIAFGAIGRKAITDDPK 217

Query: 288 WARGFYYDSIPPHSGMKLAREIATVTYRSGPEWEKRFGRKRADPSKQPALCPDFLIETYL 347
           W  G YY    P  G+ LAR I  +TY S    +K+FGR      KQ  + PD      +
Sbjct: 218 WNGGNYYGKKTPAQGLALARMIGHITYLSDASMQKKFGR-----DKQEKVGPD------M 266

Query: 348 DHAGEKFCLEYDANSLLYISKAMDLFDLGLTQQLATKKQRAEAQAKISSGTNTVNDASCS 407
                K   E    +    S          T    + +  ++  +K SS T++   +  S
Sbjct: 267 PKISSKVSSEVSPAASSKTSSETSPETSSKTSSKTSSETSSKTSSKTSSKTSSKTSSETS 326

Query: 408 LTLPEQPYQEQ-PSASTSAEQSASASETG------------------------SAPNDLV 442
                + + E  P  S+  +  +  +  G                        S    L+
Sbjct: 327 SETSSKTFSETFPDRSSHFQVESYLNHQGDTFTKRFDANSYLYITKAVDFFDLSKNGSLI 386

Query: 443 AGLAPLKDHQVLVIGVASDILFPAWQQREIAETLIQAG-NKTVEHIELGNDVSLFGHDTF 501
            GL+ +   + LVI + SD L+P +Q +EI   L   G +   E I      S +GHD F
Sbjct: 387 EGLS-VVTAKYLVISITSDWLYPPYQSQEIVSALTANGVDAKYEEIR-----SQYGHDAF 440

Query: 502 LLDVKNVGGAVRKFL 516
           LL+   +   +R FL
Sbjct: 441 LLEEGQLNYLIRGFL 455


Lambda     K      H
   0.316    0.132    0.397 

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: 600
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 517
Length of database: 579
Length adjustment: 36
Effective length of query: 481
Effective length of database: 543
Effective search space:   261183
Effective search space used:   261183
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis