Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_011770893.1 PING_RS13510 citrate synthase
Query= BRENDA::Q9I5E3 (375 letters) >NCBI__GCF_000015285.1:WP_011770893.1 Length = 436 Score = 187 bits (474), Expect = 6e-52 Identities = 115/368 (31%), Positives = 192/368 (52%), Gaps = 21/368 (5%) Query: 26 GQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYLKKLQGQRDLPQALKE 85 G++G L YRGY + LA + + E AYL+L GELPN+ QL+ + K + + + +K+ Sbjct: 72 GEKGI-LRYRGYPIEQLAEKSTYLETAYLILNGELPNQTQLNGWHKDIMAHTFIHENIKK 130 Query: 86 VLERIPKDAHPMDVMRTGASVLGTLEPELSFDQQRDVADR----LLAAFPAIMTYWYRFT 141 +++ DAHPM + + L T P+ + DR L+A P + + YR + Sbjct: 131 LIDSFHYDAHPMGTLVGTVAALSTFYPDAKNIHDQACRDRQIWRLIAKMPTLAAFSYRHS 190 Query: 142 HEGQRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSLILYAEHEFNASTFTA 196 + + IG +F+++L K +P+ + K +NV IL+A+HE N T Sbjct: 191 IGLPYVYPDQSLSYIG-NFMSMLWKKSELQYQPNPILEKAINVLFILHADHEQNCGTSVM 249 Query: 197 RVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQEATAELLKMLERKD-- 254 R AS SD +S + AI +L GPLHGGANEA + ++ S + E +K ++ + Sbjct: 250 RAVASAYSDPFSATSSAIAALYGPLHGGANEAVLHMLAEIGS-VDRVPEFIKTVKSGEVS 308 Query: 255 KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSEAIDKTMWE-----QKKLFP 309 ++MGFGH +YK+ DPR ++ K + ++ G L A++ +++ + + L+P Sbjct: 309 RLMGFGHRVYKEYDPRAKICKTLANEVFSVTGVNPLLAIALELERVALQDDYFISRHLYP 368 Query: 310 NADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTA--HVFEQRANNRIIRPSAEYTGVEQR 367 N DFY Y MG P +F +F +R +GW A F +++I RP Y G E R Sbjct: 369 NVDFYSGLIYQAMGFPVGMFPVLFAIARNTGWLAQWQEFLVDPDHKIARPRQIYCGSEVR 428 Query: 368 AFVPLEQR 375 ++ +++R Sbjct: 429 DYIAVDKR 436 Lambda K H 0.319 0.134 0.396 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: 367 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 436 Length adjustment: 31 Effective length of query: 344 Effective length of database: 405 Effective search space: 139320 Effective search space used: 139320 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