Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__HerbieS:HSERO_RS17580 Length = 440 Score = 237 bits (604), Expect = 6e-67 Identities = 157/435 (36%), Positives = 228/435 (52%), Gaps = 57/435 (13%) Query: 10 YHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLI 69 +H N S+ P+ V GEG + D +G YID G AV+ LGH HP V+EA+++QV L Sbjct: 5 FHRNPRSKLPMA-VAGEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELA 63 Query: 70 HCSNLYYNE-PQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCT 122 + ++ P E A +LA+AAP LN V+F + G+E+VE A+KLAR++ Sbjct: 64 YAHTSFFTTAPAEELAAMLADAAPGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRR 123 Query: 123 KFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVP-----------YGDVNAVEK 171 IA +HG T+GAL+ RE F P++ E HV DV V++ Sbjct: 124 HIIARRQSYHGNTLGALAIGGNAWRREMFMPMLIEAHHVSPCYAYRNRADGESDVQYVQR 183 Query: 172 AID-----------DDTAAVIVEPVQGEAGVRIPPEG-FLRELRELCDEHGLLLIVDEVQ 219 D D A + E V G +PP G + R++R +CD++G+LLI+DEV Sbjct: 184 LADELEQKILSLGADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVM 243 Query: 220 SGMGRTGQFFAFEHEDVLPDIVCLAKGLGGGV-PVGATIAREEVAEAFEPG----DHGST 274 SGMGRTG FA E + V+PDIV +AKGLG G P+GA I + + +A G HG T Sbjct: 244 SGMGRTGYLFACEEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHT 303 Query: 275 FGGNPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSEA---EDVVEEVRGRGLMMGV 331 + G+ ACAA A T+ EE L E ++G+ L +A + V ++RGRGL +GV Sbjct: 304 YIGHATACAAAVAVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGV 363 Query: 332 EVGDDERAK-----------DVAREMLDRGALV-------NVTSGDVIRLVPPLVIGEDE 373 E+ + +K V E + RG LV + +GD I L PP + ++ Sbjct: 364 ELVAERSSKLPLSPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSND 423 Query: 374 LEKALAELADALRAS 388 + + + L+DA+ AS Sbjct: 424 ISEIVQRLSDAVAAS 438 Lambda K H 0.318 0.137 0.405 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: 401 Number of extensions: 25 Number of successful extensions: 6 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: 389 Length of database: 440 Length adjustment: 31 Effective length of query: 358 Effective length of database: 409 Effective search space: 146422 Effective search space used: 146422 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: 50 (23.9 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