Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate CCNA_01983 CCNA_01983 citrate synthase
Query= BRENDA::Q8NSL1 (383 letters) >FitnessBrowser__Caulo:CCNA_01983 Length = 426 Score = 194 bits (493), Expect = 4e-54 Identities = 116/361 (32%), Positives = 176/361 (48%), Gaps = 10/361 (2%) Query: 33 LTYRGYAVEDLVENCSFEEVFYLLWHGELPTAQQLAEFNERGRSYRSLDAGLISLIHSLP 92 L +RGY ++ L E SF EV YLL +GELP A + A+F + L A Sbjct: 66 LLHRGYPIDQLAEKSSFLEVCYLLLNGELPKADEFAKFEHNITYHTMLHAQFDRFFEGFR 125 Query: 93 KEAHPMDVMRTAVSYMGTKDSEYFTTDSEHIRKVG-HTLLAQLPMVLAMDIRRRKGLDII 151 ++AHPM VM AV + S+ D R++ H L+A++P + A + G + Sbjct: 126 RDAHPMAVMTGAVGALSAFYSDSINVDDAREREISAHRLIAKMPTIAARAYKYTVGQPFV 185 Query: 152 APDSSKSVAENLLSMVFGTGPESPASNPADVRDFEKSLILYAEHSFNASTFTARVITSTK 211 +P + S +EN L M F E NP R ++ IL+A+H NAST T R+ S+ Sbjct: 186 SPRNDLSYSENFLRMCFAVPAEDWKPNPVLTRAMDRIFILHADHEQNASTSTVRLAGSSG 245 Query: 212 SDVYSAITGAIGALKGPLHGGANEFVMHTMLAIDDPNKAAAWINNALDNKNVVMGFGHRV 271 + ++ I I L GP HGGAN+ + + I + ++ D K +MGFGHRV Sbjct: 246 AHPFACIAAGIACLWGPSHGGANQEALEMLETIGSVDNIKDYVQGVKDRKYKLMGFGHRV 305 Query: 272 YKRGDSRVPSMEKSFRELAAR--HDGEKWVAMYEN-----MRDAMDARTGIKPNLDFPAG 324 YK D R M+K+ E+ A H+ + + + + + D + PN+DF +G Sbjct: 306 YKNFDPRAKVMQKTAHEVLAELGHNNDPLLQVAQELEKVALNDPYFVDRKLYPNIDFYSG 365 Query: 325 PAYHLLGFPVDFFTPLFVIARVAGWTAHIVEQYEN--NSLIRPLSEYNGEEQREVAPIEK 382 +GFP + FT LF +AR GW + E +E+ + RP Y G R+ ++K Sbjct: 366 ITLRAMGFPTNMFTVLFALARTVGWISQWKEMFEDPTRKIGRPRQLYTGATHRDYVTLDK 425 Query: 383 R 383 R Sbjct: 426 R 426 Lambda K H 0.318 0.133 0.388 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: 388 Number of extensions: 19 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: 383 Length of database: 426 Length adjustment: 31 Effective length of query: 352 Effective length of database: 395 Effective search space: 139040 Effective search space used: 139040 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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