Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate 7025360 Shewana3_2520 aminotransferase (RefSeq)
Query= curated2:Q89VE9 (405 letters) >FitnessBrowser__ANA3:7025360 Length = 452 Score = 160 bits (405), Expect = 7e-44 Identities = 131/425 (30%), Positives = 210/425 (49%), Gaps = 58/425 (13%) Query: 13 LPVFARSDLGFERGEGCWLIATNGDRYLDFTSGVAVNALGHAHPALVKALQEQATKLWHM 72 LPV+ G +GC L +G + +D TS G+ HPA++ A++ Q +L H+ Sbjct: 25 LPVY-----GVHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMERQLHQLSHV 79 Query: 73 SNLFQSPDGEKLATRLCNESFA------DFVFFCNSGAEALEGVIKLVRHHHFSKGHP-- 124 +F E T LC + A VF C+SG+ A+E IK+ + + P Sbjct: 80 --MFGGITHEPAIT-LCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQYWQGQDLPLA 136 Query: 125 ---ERYRIITFEGAFHGRTLATLAAT---GSAKYLEG---------------FGPPMDGF 163 ++ RI+T + +HG T A ++ G + G FG P+ Sbjct: 137 QKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVTKQCFVDAPQTPFGEPLRQD 196 Query: 164 DQVPHGDIEAVKKAIGPQTAGILIEPI-QGEGGVRSATPAFLKALRQLCDEKGLLLAFDE 222 D P ++ + + P+ A ++IEPI QG GG+R + +L+ LR LCDE +LL DE Sbjct: 197 DLAP---MQRILREQHPEIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDE 253 Query: 223 VQTGMGRTGDLFAHRRTGVTPDVMSLAKALGGGF-PIGAILATADAAAGM-----GPGSH 276 + TG GRTG LFA+ +TPD++ L KAL GG+ + A L T + A G+ G H Sbjct: 254 IATGFGRTGKLFAYEHADITPDILCLGKALTGGYISLAATLCTDNVAQGISQSPAGVFMH 313 Query: 277 GSTFGGNPLAIAAANAVLDVMLKPGFFDHVQKMSLLLKQKLASVIDRHGDVVSEVRGEGL 336 G TF GNPLA AAA A LD++ + + V + ++++LA ID V EVR Sbjct: 314 GPTFMGNPLACAAACASLDLINQQEWPAQVAAIEQQMQRELADAIDIPS--VKEVR---- 367 Query: 337 LIGIKAVVPSGDLV--AALRNEKL---LTVGAGDNVVRFLPPLIVTEAEIEDSVGRLERA 391 ++G V+ V AAL+ + + + V N++ +PP +++ +++ +++ Sbjct: 368 VLGAVGVLEMHQAVNTAALQQQFVDLGVWVRPFANLIYIMPPYVISSSQLTRLTQAMKQV 427 Query: 392 CAAIS 396 A I+ Sbjct: 428 AATIA 432 Lambda K H 0.320 0.137 0.404 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: 420 Number of extensions: 18 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: 405 Length of database: 452 Length adjustment: 32 Effective length of query: 373 Effective length of database: 420 Effective search space: 156660 Effective search space used: 156660 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: 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