Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate WP_089303059.1 CHB84_RS19235 acetylornithine transaminase
Query= uniprot:A0A806JQF3 (400 letters) >NCBI__GCF_900188115.1:WP_089303059.1 Length = 395 Score = 455 bits (1171), Expect = e-133 Identities = 231/390 (59%), Positives = 277/390 (71%) Query: 7 TTATMRQRWQAVMMNNYGTPPIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVI 66 T R RW++ ++NNYGTPPI + G+G V D DG Y+DLL GIAVN LGH HPAV+ Sbjct: 2 TNEQARLRWESALVNNYGTPPIEVVRGEGTRVWDADGNAYLDLLAGIAVNALGHAHPAVV 61 Query: 67 EAVTRQMSTLGHTSNLYATEPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLSRL 126 +AV+RQ++TLGHTSNL A + L+E L+ + G +V NSG+EANE A K+SRL Sbjct: 62 DAVSRQIATLGHTSNLVANPVALELSETLLEVAGLAGDGKVLLVNSGSEANEVALKISRL 121 Query: 127 TGRTKLVAAHDAFHGRTMGSLALTGQPAKQTPFAPLPGDVTHVGYGDVDALAAAVDDHTA 186 TGR +VA FHGRTMG+L LTGQPAKQ PFAPL + HV +GD+DAL AAVD TA Sbjct: 122 TGRGSVVACESGFHGRTMGALTLTGQPAKQEPFAPLVPGIGHVPFGDIDALRAAVDSDTA 181 Query: 187 AVFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITP 246 AVF+EPI GE+GV+ P GYL AAR+IT + GALLVLDEVQTG+GRTG++FA Q GI P Sbjct: 182 AVFVEPIQGEAGVIPAPDGYLRAAREITEQHGALLVLDEVQTGIGRTGSWFAFQQAGIVP 241 Query: 247 DVVTLAKGLGGGLPIGACLAVGPAAELLTPGLHGSTFGGNPVCAAAALAVLRVLASDGLV 306 DVVTLAKGLGGGLP+GA + VG AA+LL PG HG TFGGNPVC AA LAVLR + S+ L Sbjct: 242 DVVTLAKGLGGGLPLGAVIGVGGAADLLQPGQHGVTFGGNPVCCAAGLAVLRTIESESLA 301 Query: 307 RRAEVLGKSLRHGIEALGHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAAAP 366 A +GK + +EAL HP I VRG GLLLG+AL + AR AGYLVN P Sbjct: 302 EHARTVGKDIAASVEALRHPSIAGVRGAGLLLGVALREQPSAAVAGAARRAGYLVNPVTP 361 Query: 367 DVIRLAPPLIIAEAQLDGFVAALPAILDRA 396 D +RLAPPL++A FV+ LP ILD A Sbjct: 362 DTLRLAPPLVLAAEDAHRFVSDLPQILDDA 391 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: 501 Number of extensions: 22 Number of successful extensions: 1 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 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