Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_011869267.1 MMARC5_RS07725 homocitrate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000016125.1:WP_011869267.1 Length = 386 Score = 362 bits (930), Expect = e-104 Identities = 185/365 (50%), Positives = 250/365 (68%), Gaps = 1/365 (0%) Query: 5 IFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGL 64 ++DTTLRDGEQTPGV T + KLEIAKKLDEL + IEAG I S+ ER+ IK IT EGL Sbjct: 20 LYDTTLRDGEQTPGVCFTHDQKLEIAKKLDELKIKQIEAGFPIVSENERKAIKSITGEGL 79 Query: 65 NAEICSFVRALPVDIDAALECDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAVEYAK 124 NA+I + R L DID A+ECDVD + + SP+H+KYKL K+ DEV E +KAVEYAK Sbjct: 80 NAQILALSRVLKEDIDKAIECDVDGIITFIAASPMHLKYKLHKSLDEVEEMGMKAVEYAK 139 Query: 125 EHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKKITEN 184 +HGL V SAEDATR+ V LI++ E+ GA+RV + DT+G TPQ + +++ N Sbjct: 140 DHGLFVAFSAEDATRTPVEDLIRIHKNAEEHGANRVHIADTLGCATPQAMYHICSELSSN 199 Query: 185 V-NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALKILYG 243 + + VHCHNDFG A N+ ++GGA TVNGIGERAGNA++EE+V ALK+LY Sbjct: 200 LKKAHIGVHCHNDFGFAVINSIYGLIGGAKAVSTTVNGIGERAGNAAIEEIVMALKVLYD 259 Query: 244 YDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIKNTETYEPIKP 303 +D + E L E+S++V K+ +P NK +VG+ AF HE+GIHVD +++N TYEP P Sbjct: 260 HDMGLNTEILTEISKLVENYSKIRIPENKPLVGEMAFYHESGIHVDAVLENPLTYEPFLP 319 Query: 304 EMVGNRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGDLGKYISDADLLA 363 E +G +R+IILGKHSG +A+ ++L +G+ S E+L +I ++ KE + G ISD Sbjct: 320 EKIGQKRKIILGKHSGCRAVAHRLQELGLEASREELWEIVKKTKETREEGTEISDEVFKN 379 Query: 364 IVREV 368 IV ++ Sbjct: 380 IVDKI 384 Lambda K H 0.316 0.136 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: 521 Number of extensions: 22 Number of successful extensions: 2 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: 491 Length of database: 386 Length adjustment: 32 Effective length of query: 459 Effective length of database: 354 Effective search space: 162486 Effective search space used: 162486 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: 51 (24.3 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