Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011868300.1 MMARC5_RS02690 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000016125.1:WP_011868300.1 Length = 514 Score = 501 bits (1291), Expect = e-146 Identities = 242/493 (49%), Positives = 360/493 (73%), Gaps = 9/493 (1%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 +VRV DTTLRDGEQTPGVSL P +K+ IA + +G D IEAG ++SEGE+E I+KITS Sbjct: 23 KVRVFDTTLRDGEQTPGVSLMPNQKIDIAKHLSEIGVDAIEAGFPVSSEGEQESIKKITS 82 Query: 62 EGLRAEICSFARAVREDIDAAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAVDCTE 121 GL AEIC RAV++DID AI C VDS+H + TS LH E+KL+ ++E++++ A++ E Sbjct: 83 MGLDAEICGLTRAVKKDIDIAIDCGVDSIHTFIATSPLHREYKLKMSKEKIIDTAIEAIE 142 Query: 122 YAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTP-ERSYEFYRG 180 Y + G++VE SAED+TR+++D+L+ ++++ +EAGA+RI DTVG++ P +Y Sbjct: 143 YIKERGVIVEFSAEDATRTELDYLKEVYKKAVEAGADRINVPDTVGVMVPNSMNYLISEL 202 Query: 181 LSELGAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEEVVVALKSL 240 ++ PLSVHCHNDFG+AV+NS+A + AGA +VH T+NG+GERAGNA+LEE V+ L + Sbjct: 203 KKDIKVPLSVHCHNDFGIAVSNSVAAVEAGAEQVHCTVNGLGERAGNASLEETVMTLNMV 262 Query: 241 YDVDTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADGVLKKAETYEPI 300 Y ++T+++ +ML + SR+V+ TG+ QPNKAIVGEN+FAHESGIHA GVL A TYEPI Sbjct: 263 YGIETNVDTKMLTKLSRIVSNYTGIKTQPNKAIVGENSFAHESGIHAHGVLAHALTYEPI 322 Query: 301 TPEMVGHGRGFVMGKHIGTHALRKRLDELGMKVAD----DKLMEIFRRVKTLGDMGKCVT 356 P +VG+ R V+GKH G HA++ +L E+G+++ D ++ +I RVK +GD GK VT Sbjct: 323 DPAIVGNKRRIVLGKHSGAHAIKSKLSEIGVEIGDNLSKEQFCDIVERVKAIGDKGKIVT 382 Query: 357 DVDLQAIAEDVL--GVMEDKVVDLQEVTIVSGNRVTPTASVKLRVDDREVLEAGTGVGPV 414 D D+ AI ED+ + +++VDL++ +++GN V PTASV L+V D+ + GVGPV Sbjct: 383 DADVMAITEDITQRTLKSERIVDLEQFAVITGNNVLPTASVALKVRDKIYKTSELGVGPV 442 Query: 415 DAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGDRIISARSTQPDIIMA 474 DAA+ AI+ ++ + ++ L EY++ AI+GGTDA+ +V ++L + ++ + A++T D++ A Sbjct: 443 DAALKAIQAAVGE--NVRLNEYNISAISGGTDAIAEVTVRLENHEKEVIAKATGDDVVKA 500 Query: 475 SVEAFLSGVNRLL 487 SVEA + G+N+L+ Sbjct: 501 SVEAVIDGINKLM 513 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: 748 Number of extensions: 35 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: 514 Length adjustment: 34 Effective length of query: 462 Effective length of database: 480 Effective search space: 221760 Effective search space used: 221760 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 Apr 10 2024. The underlying query database was built on Apr 09 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