Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate AO356_07855 AO356_07855 hypothetical protein
Query= BRENDA::Q9X266 (343 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07855 Length = 353 Score = 259 bits (663), Expect = 6e-74 Identities = 155/348 (44%), Positives = 206/348 (59%), Gaps = 10/348 (2%) Query: 2 IDLRSDTVTKPTEEMRKAMAQAEVGDDVYGEDPTINELERLAAETFGKEAALFVPSGTMG 61 IDLRSDTVTKPTE MRKA+ QAEVGDD +GEDPT+ LE A F KEAALF GT+ Sbjct: 3 IDLRSDTVTKPTEGMRKAIYQAEVGDDCFGEDPTVRALEEYCANYFQKEAALFTSGGTLS 62 Query: 62 NQVSIMAHTQRGDEVILEADSHIFWYEVGAMAVLSGVMPHPVPGKNGAMDPDDVRKAIRP 121 NQ++I A T GDE+ L+A HI +YE + + SGV NG D D+ K Sbjct: 63 NQLAIKALTNPGDEIFLDASYHINFYESASTSAFSGVNFSLSNHDNGLFDVADLEKLHAS 122 Query: 122 R-----NIHFPRTSLIAIENTHNRSGGRVVPLENIKEICTIAKEHGINVHIDGARIFNAS 176 + N PR ++ IENT GG + PL+ + ++ AK+ G ++DGARI +AS Sbjct: 123 KCRWSQNYALPR--VVVIENTLGCKGGDIFPLQQMNDVFAYAKDIGAYRYLDGARILHAS 180 Query: 177 IASGVPVKEYAGYADSVMFCLSKGLCAPVGSVVVGDRDFIERARKARKMLGGGMRQAGVL 236 IASG+ V Y AD + CLSKGL AP+GS++VG ++ I RA+K RK GG + QAG++ Sbjct: 181 IASGIDVTSYTDNADLLSMCLSKGLGAPIGSIMVGSQELILRAKKYRKWFGGDLHQAGMM 240 Query: 237 AAAGIIALTKMVDRLKEDHENARFLALKLKEIGYSVNPEDVK-TNMVILRTDNLKVNAHG 295 AAAG+ A+ V+RL +DHE+A L L +I + P K TNMV L L V Sbjct: 241 AAAGLYAMQNHVERLADDHEHAALLHQLLNDIDEA--PARYKGTNMVTLDISALGVAPVQ 298 Query: 296 FIEALRNSGVLANAVSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKFS 343 F LR GV + E+R + H ++SR+DI +A I + R+ S Sbjct: 299 FAALLRQKGVGGLPYNAREMRFMPHLNISRDDIHKAAGIIKATVRELS 346 Lambda K H 0.319 0.135 0.384 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: 299 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: 343 Length of database: 353 Length adjustment: 29 Effective length of query: 314 Effective length of database: 324 Effective search space: 101736 Effective search space used: 101736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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