Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate WP_027490798.1 LRK54_RS04480 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q7W7H6 (393 letters) >NCBI__GCF_021560695.1:WP_027490798.1 Length = 439 Score = 178 bits (451), Expect = 3e-49 Identities = 145/414 (35%), Positives = 199/414 (48%), Gaps = 49/414 (11%) Query: 19 GRGVWLWDTGERRYLDALAGIGVSCLGHGHPGLVAAISEQAARLIHTSNIYEVPQQAALA 78 GRG +L RR LD + S LGH HP +VAAI EQA +L ++ + +A LA Sbjct: 26 GRGAYLELEDGRRILDMSSLAECSNLGHQHPAVVAAIREQAQQLCFVTSAWGAQPRAELA 85 Query: 79 RRLAELSGM--SEVLFSNSGSEANEAAIKLARYYGYKQGNTHAHIITMDSSWHGRTLATL 136 L E +G V F+ +G++ANE A+K AR G G HI+T D S+HG + A + Sbjct: 86 DALLEKAGFDGGRVFFTLAGADANENAVKFARQAG---GKPRGHIVTRDRSYHGASYACM 142 Query: 137 AATGSDKARQGFGPMPSGFIQVPYNDL-------PAIRAAGE-------------AEPRV 176 A +G + R P G + VP D +A GE V Sbjct: 143 ALSGDARTRSQVDPGAFGVLHVPPPDTYRCPFGSEDAQACGEHAVATVAQTIDHHGASSV 202 Query: 177 TAVLLEVLQGEGGIRPSDMAFLRGVRQLCTERGWLLMIDEVQSGIGRTGKWFAHQ-WADI 235 AVL+E G GI D + G+R+L ERG L+ DEV SG GR G+WFA Q D Sbjct: 203 AAVLMEPNAGTNGIVAPD-NYWPGLRKLTRERGVYLIADEVMSGFGRCGEWFAWQRHGDA 261 Query: 236 -RPDVMTLAKGLAGG-VPIGAMLAAGPAAGVFAPGS--HGTTFGGGPLACAAGLAVIDAI 291 +PD+MTLAKGL G +P+GA++ + P A G T+ G PL+CAAGLA + A Sbjct: 262 GKPDLMTLAKGLTGAHLPLGAVVLSAPVAARLQHEMLYTGLTYCGHPLSCAAGLAALRAY 321 Query: 292 EQEGLLANAHEVGAHLHAALASELAGVPGIIEVR-GHGLMLGIEL--------------- 335 E E L+A + +G + A L + A P I +VR GHGL +EL Sbjct: 322 EVEDLIARSRILGGWMLAELRALQARHPVIGDVRGGHGLFAVVELVENRDTRAPLAPWPQ 381 Query: 336 -DRPCGILATRAMEAGLLINVTRERVVRLLPPLILSGEEADQIVRILVPLIKQF 388 L AM G+ +R ++ L PPL++ + +L L+ F Sbjct: 382 TPPALSALVDAAMAQGVSF-ASRGNLLLLAPPLVIENHALADALSLLDRLLAHF 434 Lambda K H 0.320 0.137 0.411 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: 415 Number of extensions: 20 Number of successful extensions: 5 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: 393 Length of database: 439 Length adjustment: 31 Effective length of query: 362 Effective length of database: 408 Effective search space: 147696 Effective search space used: 147696 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 (21.8 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