Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate SMc02413 SMc02413 aminotransferase
Query= curated2:A0QYS9 (390 letters) >FitnessBrowser__Smeli:SMc02413 Length = 437 Score = 217 bits (553), Expect = 4e-61 Identities = 151/406 (37%), Positives = 213/406 (52%), Gaps = 41/406 (10%) Query: 19 PLSLVSGEGAVVTDADGREYLDLLGGIAVNLLGHRHPAVIEAVTTQL-DTLGHTSNLYAT 77 P ++V G GA +T DGR+ LD LGH HPA+ EAV L D G + A Sbjct: 22 PQAVVGGSGAYLTADDGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSAN 81 Query: 78 EPGIALAEALVGQLGTQAR--VFFCNSGTEANE-VAFKITRLTGKTKIVAAEGAFHGRTM 134 E + LAE L+ + +AR V+F +SG++ANE VA + TG+ +I+A GA+HG T+ Sbjct: 82 EACVLLAEKLLSLVPERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGTI 141 Query: 135 GSLALTGQPSKQAP------FEPLPGNVMHVPYGDVAALEAAV------------DDQTA 176 GS+ ++G P++Q P P + + AA +AA+ ++ A Sbjct: 142 GSMGVSGHPAQQGSRAEGLTLVPYPNS--YAAGSPEAARDAALAHLERLFATEVPPEEVA 199 Query: 177 AVFLEPIMGEGGVVVPPAGYLVAAREITSKHGALLVLDEVQTGVGRTGAFFAHQHDGIVP 236 A F+EPI +GG++VPP G+ A + +HG L+V DEV+ G+GR+G F A +H GI P Sbjct: 200 AFFIEPIQSDGGMLVPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFNAFEHSGIEP 259 Query: 237 DVVTMAKGLGGGLPIGACLAVGATGDLLTPGLHGSTFGGNPVCTAAGLAVLKTLAAEDLV 296 D+V KGLGGGLPI A + A + + T GNPVC AA LAVL+T+ + L+ Sbjct: 260 DIVVFGKGLGGGLPISAVVGPEAIMN-HSVAFSLQTVHGNPVCAAAALAVLQTIERDHLI 318 Query: 297 ARAGVLGKTLSHGIEEL--GHPLVDKVRGKGLLQGIVLTVPSAKAVETAARDAGFLVNAA 354 A GK L ++ L H L+ VRG+GL GI L A E A+R A V A Sbjct: 319 LNADRSGKVLREALDRLTARHTLIGDVRGRGLALGIELVTDPASR-EPASRQAALTVYRA 377 Query: 355 ------------APEVVRLAPPLIITEGQIEAFITAL-PAVLDTAA 387 V+ L PPL +T + E+ + L A+ D AA Sbjct: 378 FQLGLVLYYVGVQSNVLELTPPLTLTPAEAESGVAMLGQALADVAA 423 Lambda K H 0.317 0.136 0.391 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: 526 Number of extensions: 31 Number of successful extensions: 6 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: 390 Length of database: 437 Length adjustment: 31 Effective length of query: 359 Effective length of database: 406 Effective search space: 145754 Effective search space used: 145754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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