Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate GFF2831 PGA1_c28770 taurine--pyruvate aminotransferase Tpa
Query= curated2:Q8R7C1 (393 letters) >FitnessBrowser__Phaeo:GFF2831 Length = 465 Score = 201 bits (511), Expect = 4e-56 Identities = 137/430 (31%), Positives = 214/430 (49%), Gaps = 57/430 (13%) Query: 17 PIMLVKGEGTRVWDSEGNAYLDFVAG-IAVNSLGHCHPALVEAIKKQAETLIHCSNLYWN 75 P ++V+G+G RVWD G +LD V+G + ++G+ + +A+ Q L + + + Sbjct: 36 PRIIVEGKGMRVWDQNGKEWLDAVSGGVWTVNVGYGREEIAKAVYDQLMKLCYFAQSAGS 95 Query: 76 EKQIELARMISENSFG-GKVFFANSGAEANEGAIKLARKYASLKYGGKRYKIITAKNSFH 134 A + E G +V++ NSG+EANE A K+ R+ A KYGGK+ KI+ +H Sbjct: 96 IPGALFAEKLIEKMPGMSRVYYNNSGSEANEKAFKMVRQIAHKKYGGKKTKILYRDRDYH 155 Query: 135 GRTFGALTATGQEKYHKGFGPLLAGFKYVP------------------------LNDIEA 170 G T A++A GQE+ + +GP F VP N IE Sbjct: 156 GSTLAAMSAGGQEERNMQYGPFAPDFVKVPHCMEYRKHELGLEHLSGKEFGIAAANQIEE 215 Query: 171 LY-EAVDDEVCAIMLEVIQGEGGIHEATPEYVKAVRKICDENDLLFILDEVQTGIGRTGK 229 + D V A+ LE + GG+ EA Y V++IC + D+L +DEV G+GRTG Sbjct: 216 IILREGPDTVGALCLEPVTAGGGVIEAPEGYWPRVQEICKQYDILLHIDEVVCGVGRTGT 275 Query: 230 LFGYEHYGVVPDIMTLAKGLGGGF-PIGAIVAKEDKAVF--------KPGDH---ASTFG 277 FGY+HYG+ PD +T+AKG+ G+ I +V E AVF P ++ STFG Sbjct: 276 WFGYQHYGIQPDFVTMAKGVASGYAAIACLVTTE--AVFDMFKDDASDPMNYFRDISTFG 333 Query: 278 GNPLACAAGIAVLNEVTKDGFLEGVDKKGKYFREGLETLQKKHKVVKEIRGKGLMVGCE- 336 G AA + + + + L+ G + LE L +KH+V+ ++RGKGL +G E Sbjct: 334 GCTAGPAAALVNMQIIEDENLLDNCTAMGARMKSNLEALMEKHQVIGDVRGKGLFIGAEL 393 Query: 337 ---------VDLEDASEIVLKALEKGLLINSVS------HNVLRFVPPLIVTEEEIDEAL 381 VD + A +V + + ++I + +N L F P LIVT E++D+ Sbjct: 394 VADRDTKEPVDEKLAQAVVAECGNQNVIIGVTNRSIPGKNNTLCFSPALIVTPEDVDKIT 453 Query: 382 QILDDVLSEI 391 +D L+++ Sbjct: 454 DAVDVALTKV 463 Lambda K H 0.319 0.139 0.405 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: 455 Number of extensions: 32 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: 393 Length of database: 465 Length adjustment: 32 Effective length of query: 361 Effective length of database: 433 Effective search space: 156313 Effective search space used: 156313 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 (21.7 bits) S2: 51 (24.3 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