Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_008346063.1 BA79_RS07510 citrate synthase
Query= SwissProt::Q8EJW2 (375 letters) >NCBI__GCF_000691145.1:WP_008346063.1 Length = 372 Score = 291 bits (745), Expect = 2e-83 Identities = 156/369 (42%), Positives = 230/369 (62%), Gaps = 7/369 (1%) Query: 11 GLRGQSAGETALSTVGVSGSGLTYRGYDVKDLAENATFEEVAYLILYGELPTTAQLAAYK 70 GL G A +++S++ LTY GY++ DL E ATFEE+ YL+ + +LP +L+ K Sbjct: 6 GLEGIVATTSSVSSI--IDDTLTYVGYNIDDLTEKATFEEIVYLLWHLKLPNEQELSELK 63 Query: 71 TKLKGMRGLPQALKEVLERIPADA-HPMDVMRTGCSMLGNLEAEHSFSEQS---QIADRL 126 +L +PQ + E + D HPM +RT S+LG L+ E ++ + A RL Sbjct: 64 QQLNENAHIPQEIIEHFKSYSLDGVHPMSAIRTAVSLLGLLDDESEIMDKEANYRKAIRL 123 Query: 127 LAAFPSIICYWYRFSHDGVRIDTETDDDQIGAHFLHLLHGKAPSALHTKVMDVSLILYAE 186 A ++ + R G+ ++ A+FL++L+G+ PS + + +D +LIL+A+ Sbjct: 124 QAKISGLVAAFSRI-RKGLEPVQPKEEYSYAANFLYMLNGEEPSPVEIEAIDKALILHAD 182 Query: 187 HEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMKDEADARDVL 246 HE NASTFTARVC +TLSD++S VT AIG+L+GPLHGGANE M+++ ++ + + + Sbjct: 183 HELNASTFTARVCVATLSDIYSGVTAAIGALKGPLHGGANEGVMKMLSEIGEVENVDSYI 242 Query: 247 MGKLERKEKIMGFGHAIYRDSDPRNAIIKEWSEKLAADYGDDRLYRVSVACEALMWEQKK 306 GKLE+KEKIMGFGH +YR DPR +KE S++L G+ + Y +SV E ++ +K Sbjct: 243 HGKLEKKEKIMGFGHRVYRQGDPRAKHLKEMSQRLTNLTGEPKWYEMSVRAEEIVTSEKN 302 Query: 307 LFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWTAHVMEQRSNNRIIRPSADYVGVSP 366 L N DF+ AS YH +GI LFTPIFV SR +GW AH++EQ NNR+IRP ADY+G Sbjct: 303 LPPNVDFYSASVYHSLGIDHDLFTPIFVISRFSGWIAHILEQYDNNRLIRPRADYIGPDL 362 Query: 367 RKVIPIANR 375 + +PI+ R Sbjct: 363 QTFVPISER 371 Lambda K H 0.320 0.134 0.401 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: 321 Number of extensions: 13 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: 375 Length of database: 372 Length adjustment: 30 Effective length of query: 345 Effective length of database: 342 Effective search space: 117990 Effective search space used: 117990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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