Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_051399596.1 AMYHA_RS06280 citrate synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_000504245.1:WP_051399596.1 Length = 438 Score = 213 bits (543), Expect = 6e-60 Identities = 129/379 (34%), Positives = 209/379 (55%), Gaps = 21/379 (5%) Query: 17 AGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQL 76 A +A++ + L YRGY + LA + F EV+YLL+YGELPT+ QL + G++ + Sbjct: 61 ATSSAITYIDGDAGILRYRGYPIEQLAEHSNFIEVSYLLIYGELPTERQLADFNGRIERH 120 Query: 77 RDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQ----DFSQQHDKTDRLLAAFPA 132 L + LK + P DAHPM V+ + S L + D T R+LA P Sbjct: 121 TLLHEDLKRFFDGFPRDAHPMPVLSSAVSALSTFYQDSLNPFDEPSVELSTVRMLAKVPT 180 Query: 133 IMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHG--KKPSELH---VKVMNVSLILYAEH 187 + Y Y+ S GQ + +S+ +FL + G +P E+ K +++ IL+A+H Sbjct: 181 LAAYAYKKS-IGQPFLYPDNSLSLVENFLRMTFGLPAEPYEIDPDIAKALDLLFILHADH 239 Query: 188 EFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTL 247 E N ST T R+ S+ ++LF+ ++A I +L GPLHGGAN A ++M+E + ++ + Sbjct: 240 EQNCSTSTVRLVGSSEANLFASVSAGINALFGPLHGGANAAVLDMLEDIRADGGDVDRFV 299 Query: 248 GMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVGDT-VLFPVSEAIDKT--- 300 + K+ ++MGFGH +YK+ DPR ++IK + ++ +G + L +++ +++T Sbjct: 300 SRVKNKEAGVRLMGFGHRVYKNYDPRAKIIKKTADEILGRLGKSDELLDIAKKLEETALS 359 Query: 301 --MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRAN--NRIIR 356 + ++KL+PN DFY Y +G PT+ FT +F RL GW AH E + +I R Sbjct: 360 DDYFVERKLYPNVDFYTGLIYRALGFPTEYFTVLFALGRLPGWIAHWREMMLDPARKIGR 419 Query: 357 PSAEYTGVEQRKFVPIEQR 375 P YTG +RK++ IE+R Sbjct: 420 PRQVYTGAPERKYLDIEKR 438 Lambda K H 0.321 0.135 0.406 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: 400 Number of extensions: 21 Number of successful extensions: 5 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: 438 Length adjustment: 31 Effective length of query: 344 Effective length of database: 407 Effective search space: 140008 Effective search space used: 140008 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 (21.9 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