Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_014265940.1 ACIX8_RS13690 citrate synthase
Query= SwissProt::O34002 (379 letters) >NCBI__GCF_000178955.2:WP_014265940.1 Length = 388 Score = 285 bits (730), Expect = 1e-81 Identities = 151/366 (41%), Positives = 223/366 (60%), Gaps = 9/366 (2%) Query: 8 KGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSELKAF 67 KGL V A+ ++I ++ D L YRG + ELA K SFE++ YLLWN LP +EL F Sbjct: 7 KGLQDVVANESSICFIDGDKGILSYRGIDIHELAEKSSFEEITYLLWNGALPTAAELNDF 66 Query: 68 VNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKAMSL 127 + + R++ ++V + + PM+V RT VS+L A + + AN+ K+ L Sbjct: 67 SHQLAAARQIPDDVIAFLRNVPKTASPMEVLRTTVSLLSIYDADEKSTLHTANIRKSFRL 126 Query: 128 LATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAAPEVVEAFNVSMILYAEH 187 A +VA R R+G+E+++P L ++ANFLWM GE+ + +A +V++IL+A+H Sbjct: 127 TAQIAMIVAIFDRIRKGKEIVKPDTSLSHAANFLWMLNGEKPSETATKALDVALILHADH 186 Query: 188 SFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGIRKDESLDEA 247 NASTF ARVI +TL+DLHSA+TGAIGALKGPLHGGANEAVMH +I D+A Sbjct: 187 ELNASTFAARVIAATLSDLHSAITGAIGALKGPLHGGANEAVMHLLYDI--------DKA 238 Query: 248 ATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYDRPEMLGLYNGLE 307 + LA K+K+ GFGHRVY D R ++ + + K + P+ + +E Sbjct: 239 GEDPVEHVRKMLANKEKISGFGHRVYTTEDPRATHLRKMSEDLGKDAN-PKWYTMSRQIE 297 Query: 308 AAMEEAKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWTAHIMEQVADNALIRPL 367 ++E K++ N+D+ + TY +G D ++FTP+F +RI+GW AH++EQ DN LIRP Sbjct: 298 LFVKEEKKLNANVDFYSASTYTTLGIDIDLFTPIFAISRISGWCAHVIEQHDDNRLIRPR 357 Query: 368 SEYNGP 373 ++Y GP Sbjct: 358 ADYTGP 363 Lambda K H 0.316 0.130 0.376 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: 377 Number of extensions: 18 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: 379 Length of database: 388 Length adjustment: 30 Effective length of query: 349 Effective length of database: 358 Effective search space: 124942 Effective search space used: 124942 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: 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