Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_037570915.1 BS73_RS08925 acetylornithine transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_000744815.1:WP_037570915.1 Length = 395 Score = 473 bits (1217), Expect = e-138 Identities = 241/388 (62%), Positives = 285/388 (73%), Gaps = 2/388 (0%) Query: 6 TTTATMRQRWQAVMMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAV 65 T + QRWQ +MNNYGTP I LA G+GA V D DG+ Y DL+ GIAVN LGH HPAV Sbjct: 2 TGNQELTQRWQQSLMNNYGTPRIPLARGEGAHVWDADGKRYTDLVAGIAVNALGHGHPAV 61 Query: 66 IEAVTRQMSTLGHTSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSR 125 + AVT Q++TLGH SNL+ EP + L+E L+ L G + RVFFCNSGAEANE AFK+ R Sbjct: 62 VGAVTEQINTLGHVSNLFIAEPPVRLSERLLELFG--RPGRVFFCNSGAEANEGAFKIGR 119 Query: 126 LTGRTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHT 185 LTGR +VA FHGRTMG+L+LTGQP KQ FAPLPGDV V YGDV+AL AAV + T Sbjct: 120 LTGRRHMVATTGGFHGRTMGALSLTGQPGKQDGFAPLPGDVEFVPYGDVEALRAAVTEET 179 Query: 186 AAVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGIT 245 A +EP+ GE+G V P GYL AAR+IT +GALLV+DEVQTG+GRTG +FAHQ GI Sbjct: 180 AFFIVEPVQGENGAVPAPDGYLEAAREITRAKGALLVVDEVQTGIGRTGHWFAHQAAGIE 239 Query: 246 PDVVTLAKGLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGL 305 PDVVTLAKGLGGGLPIGA +A G AAELL PG HG+TFGGNPVC AA LAVL +A DGL Sbjct: 240 PDVVTLAKGLGGGLPIGATVAFGAAAELLQPGQHGTTFGGNPVCCAAGLAVLDTIAQDGL 299 Query: 306 VRRAEVLGKSLRHGIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAAA 365 + + +G+ LR GIE++G PL+ VRG GLLLGI LT P A +A A+ AG+LVNA Sbjct: 300 LDHVKRVGERLRSGIESIGDPLVARVRGTGLLLGIVLTEPLAPQVQAAAQRAGFLVNATG 359 Query: 366 PDVIRLAPPLIIAEAQLDGFVAALPAIL 393 PD++RL PPL + E D F+A LP IL Sbjct: 360 PDLVRLVPPLTLPEVDADAFLAVLPGIL 387 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: 575 Number of extensions: 33 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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 Jul 26 2024. The underlying query database was built on Jul 25 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