Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_012172068.1 AZC_RS18230 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000010525.1:WP_012172068.1 Length = 526 Score = 365 bits (937), Expect = e-105 Identities = 215/504 (42%), Positives = 301/504 (59%), Gaps = 16/504 (3%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 +V + DTTLRDGEQ PG S+T EEKL +A ++ +G D+IEAG I S G+ E + +I Sbjct: 18 RVIIFDTTLRDGEQCPGASMTFEEKLEVAELLETMGVDVIEAGFPIASIGDFESVAEIAR 77 Query: 62 EGLRAEICSFARAVREDID----AAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAV 117 A I +RA DID A +H + TS +H+++KL+K +VLE V Sbjct: 78 RSKTAIIAGLSRAALNDIDRCAEAVKQAKRGRIHTFLSTSPVHMKYKLQKEPHQVLEMIV 137 Query: 118 DCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEF 177 A +H VE SAED TR++MDFL I+AGA I DTVG TP+ Sbjct: 138 ASVTRARNHVEDVEWSAEDGTRTEMDFLCRCVEAAIKAGATTINIPDTVGYTTPQEYEAL 197 Query: 178 YRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEE 232 +R + E A SVHCHND G+AVANSLAGL GA ++ TINGIGERAGNAALEE Sbjct: 198 FRTVRERVPNSDKAIFSVHCHNDLGMAVANSLAGLAGGARQIECTINGIGERAGNAALEE 257 Query: 233 VVVALKSLYDV---DTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADG 289 VV+A+ + DV T I+ +L S+MV+ +T +Q NKAIVG NAFAHESGIH DG Sbjct: 258 VVMAINTRRDVLPYRTGIDATLLTRASKMVSGVTSFPVQYNKAIVGRNAFAHESGIHQDG 317 Query: 290 VLKKAETYEPITPEMVGHGR-GFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTL 348 +LK +TYE +TPE VG + VMGKH G A R +L LG ++ ++ L + F R K L Sbjct: 318 MLKHTQTYEIMTPESVGVTKTSLVMGKHSGRAAFRDKLKALGYELGENALNDAFTRFKDL 377 Query: 349 GDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTASVKLRVDDREVLEAG 408 D K + D D++A+ + + D+ V L +++++G R A++++ VD + +E Sbjct: 378 ADRKKVIYDEDIEALVDQGIAAAYDR-VKLLSLSVIAGTRGPQRATMRIEVDGQPRIEEA 436 Query: 409 TGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGDRIISARSTQ 468 G GPVDA AIK + A LE Y V A+T GTDA +V ++L ++++AR+ Sbjct: 437 EGNGPVDATFNAIKALIPHTA--KLELYQVHAVTEGTDAQAEVSVRLAEDGKVVTARAAD 494 Query: 469 PDIIMASVEAFLSGVNRLLANEKS 492 PD ++AS +A+++ +N+L +S Sbjct: 495 PDTLVASAQAYITALNKLSVKRQS 518 Lambda K H 0.317 0.135 0.373 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: 631 Number of extensions: 33 Number of successful extensions: 7 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: 496 Length of database: 526 Length adjustment: 35 Effective length of query: 461 Effective length of database: 491 Effective search space: 226351 Effective search space used: 226351 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: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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