Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011385142.1 AMB_RS13895 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8TUZ5 (389 letters) >NCBI__GCF_000009985.1:WP_011385142.1 Length = 439 Score = 191 bits (485), Expect = 3e-53 Identities = 142/432 (32%), Positives = 226/432 (52%), Gaps = 51/432 (11%) Query: 1 MDARELIDKYHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEA 60 +DAR + + ++ + + G+ ++ +G EY+DLV+ VN+ GH +PA+ +A Sbjct: 11 LDARHVWHPFTQAGTAQPAILALGARGSTIYAADGREYLDLVSSWWVNLHGHANPAIAQA 70 Query: 61 VKEQVERLIHCSNL-YYNEPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF- 118 V +Q RL + +EP A A + + P DLN+VF+ + G+ +VE A+KLA ++ Sbjct: 71 VADQAGRLEQVIFADFTHEPAARLAHRVCKRLPGDLNRVFYSDDGSTAVEVALKLAHQYW 130 Query: 119 ----TGCTKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHVPY-----GDVNAV 169 + +IAFEGG+HG T GA+SA + ++ ++ E VP+ GD Sbjct: 131 RNHGQHRSTYIAFEGGYHGDTAGAMSAGHSSGYFGAWKEMLFPVETVPFPATWNGDETVE 190 Query: 170 EK------AID-------DDTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIV 215 +K A+D D AAVI+EP +QG +G+R+ FLR+L ++G LLI+ Sbjct: 191 DKEQAALDALDLLFAANPDHVAAVIIEPLIQGASGMRMCRPDFLRKLEAKVRDNGSLLIL 250 Query: 216 DEVQSGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD---- 270 DEV +G GRTG+ FA + PD++CL+KGL GG +P+ T+AR+ + EAF D Sbjct: 251 DEVMTGFGRTGEIFACVKAGITPDLICLSKGLTGGFLPLSVTVARDGIFEAFLGQDLSRA 310 Query: 271 --HGSTFGGNPLACAAVCAAV----STVLEENLP--EAAERKGKLAMRILSEAED----- 317 HG ++ NPL CAA ++ S ++ + EA R+ ++ LS Sbjct: 311 FLHGHSYTANPLGCAAGLTSIDLLESAACQQRIGAIEAIHRRRLDGLKGLSNVAHTRLTG 370 Query: 318 --VVEEVRGRGLMMGVEVGDDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELE 375 +V G G G E G + K L+RG L+ G+V+ L+PP I + ELE Sbjct: 371 TVAALDVIGGG--KGYEAGIGPKLK---AAFLERGLLLR-PLGNVLYLLPPYCITDAELE 424 Query: 376 KALAELADALRA 387 +A + + LR+ Sbjct: 425 RAWDAVDEVLRS 436 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: 424 Number of extensions: 25 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: 389 Length of database: 439 Length adjustment: 31 Effective length of query: 358 Effective length of database: 408 Effective search space: 146064 Effective search space used: 146064 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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