Align Acetylornithine aminotransferase; Short=ACOAT; EC 2.6.1.11 (characterized, see rationale)
to candidate SMc02413 SMc02413 aminotransferase
Query= uniprot:A0A806JQF3 (400 letters) >FitnessBrowser__Smeli:SMc02413 Length = 437 Score = 228 bits (581), Expect = 3e-64 Identities = 160/407 (39%), Positives = 216/407 (53%), Gaps = 39/407 (9%) Query: 27 PIALASGDGAVVTDVDGRTYIDLLGGIAVNVLGHRHPAVIEAVTRQMSTLGHTSNLY-AT 85 P A+ G GA +T DGR +D LGH HPA+ EAV R +S S L A Sbjct: 22 PQAVVGGSGAYLTADDGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSAN 81 Query: 86 EPGIALAEELVALLGADQRTRVFFCNSGAEANEAAFKLS-RLTGRTKLVAAHDAFHGRTM 144 E + LAE+L++L+ R RV+F +SG++ANE ++ TGR +++A H A+HG T+ Sbjct: 82 EACVLLAEKLLSLVPERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGTI 141 Query: 145 GSLALTGQPAKQTPFA------PLPGDVTHVGYGDV--DALAAAVD---------DHTAA 187 GS+ ++G PA+Q A P P G + DA A ++ + AA Sbjct: 142 GSMGVSGHPAQQGSRAEGLTLVPYPNSYA-AGSPEAARDAALAHLERLFATEVPPEEVAA 200 Query: 188 VFLEPIMGESGVVVPPAGYLAAARDITARRGALLVLDEVQTGMGRTGAFFAHQHDGITPD 247 F+EPI + G++VPP G+ A + R G L+V DEV+ G+GR+G F A +H GI PD Sbjct: 201 FFIEPIQSDGGMLVPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFNAFEHSGIEPD 260 Query: 248 VVTLAKGLGGGLPIGACLAVGPAAEL-LTPGLHGSTFGGNPVCAAAALAVLRVLASDGLV 306 +V KGLGGGLPI A VGP A + + T GNPVCAAAALAVL+ + D L+ Sbjct: 261 IVVFGKGLGGGLPISA--VVGPEAIMNHSVAFSLQTVHGNPVCAAAALAVLQTIERDHLI 318 Query: 307 RRAEVLGKSLRHGIEAL--GHPLIDHVRGRGLLLGIALTAPHAKDAEATARDAGYLVNAA 364 A+ GK LR ++ L H LI VRGRGL LGI L A E +R A V A Sbjct: 319 LNADRSGKVLREALDRLTARHTLIGDVRGRGLALGIELVTDPA-SREPASRQAALTVYRA 377 Query: 365 ------------APDVIRLAPPLIIAEAQLDGFVAAL-PAILDRAVG 398 +V+ L PPL + A+ + VA L A+ D A G Sbjct: 378 FQLGLVLYYVGVQSNVLELTPPLTLTPAEAESGVAMLGQALADVAAG 424 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: 510 Number of extensions: 28 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: 400 Length of database: 437 Length adjustment: 32 Effective length of query: 368 Effective length of database: 405 Effective search space: 149040 Effective search space used: 149040 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