Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_011842390.1 RSPH17029_RS17535 aspartate aminotransferase family protein
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000015985.1:WP_011842390.1 Length = 442 Score = 205 bits (522), Expect = 2e-57 Identities = 157/433 (36%), Positives = 219/433 (50%), Gaps = 59/433 (13%) Query: 24 GTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHT-SNL 82 G+ P+A A G+G + D +GR Y+D GG AV+ LGH + AV A+ Q+ L + Sbjct: 12 GSLPVA-AEGEGCYILDAEGRRYLDGSGGAAVSCLGHSNAAVRAALHDQLDRLAFAHTGF 70 Query: 83 YATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRL-------TGRTKLVAA 135 + +EP LA+ L A + RV+ + G+EA EAA KL+R GR +++A Sbjct: 71 FTSEPAERLADRLAAA-APEGIERVYLVSGGSEAVEAALKLARQYFMEVGQPGRHRVIAR 129 Query: 136 HDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVG----------------YG-----DV 174 ++HG T+G+LA G ++ FAPL + +HV YG ++ Sbjct: 130 RQSYHGNTLGALAAGGNEWRRAQFAPLLVETSHVSPCYEYRGRAEDESLEAYGLRVADEL 189 Query: 175 DALAAAVDDHTAAVFL-EPIMGESGVVVPPA-GYLAAARDITARRGALLVLDEVQTGMGR 232 +A + T F+ EP++G + VP GYL R+I R G LL+LDEV GMGR Sbjct: 190 EAEIQRLGPETVMAFVAEPVVGATAGAVPAVPGYLKRIREICDRHGVLLILDEVMCGMGR 249 Query: 233 TGAFFAHQHDGITPDVVTLAKGLGGGL-PIGACLAVGPAAELLTPG----LHGSTFGGNP 287 TG FA DG+ PD++T+AKGLG G PIGA L G + + G HG T+ G+ Sbjct: 250 TGHLFACAEDGVAPDMITIAKGLGAGYQPIGALLVQGRLYDAIAAGSGFFQHGHTYMGHA 309 Query: 288 VCAAAALAVLRVLASDGLVRRAEVLGKSLRHGI-EALG-HPLIDHVRGRGLLLGIALTAP 345 + AAAA AVL + L++ G L + E LG HP + +RGRGL GI L A Sbjct: 310 MAAAAANAVLDEIEGRDLLQAVRRQGARLEGLLQERLGQHPHVGDIRGRGLFRGIELVAD 369 Query: 346 -------------HAK-DAEATA-----RDAGYLVNAAAPDVIRLAPPLIIAEAQLDGFV 386 HA+ AEA A G ++ D I LAPP II+ A+L+ V Sbjct: 370 RETKEPFDPARKLHARIKAEAFAGGLICYPMGGTLDGVRGDHILLAPPFIISNAELEELV 429 Query: 387 AALPAILDRAVGA 399 L LDRA+ A Sbjct: 430 DKLSGALDRALAA 442 Lambda K H 0.320 0.136 0.399 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: 549 Number of extensions: 31 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: 400 Length of database: 442 Length adjustment: 32 Effective length of query: 368 Effective length of database: 410 Effective search space: 150880 Effective search space used: 150880 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 16 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