Align acetylornithine transaminase (EC 2.6.1.11) (characterized)
to candidate WP_055068491.1 M72_RS12800 aspartate aminotransferase family protein
Query= BRENDA::A8J933 (460 letters) >NCBI__GCF_001406815.1:WP_055068491.1 Length = 399 Score = 323 bits (827), Expect = 8e-93 Identities = 177/404 (43%), Positives = 249/404 (61%), Gaps = 11/404 (2%) Query: 55 KQVIADESKYVLQTYGRAPVVISHGKGAKMWDVEGKEYIDMAAGIAVNALGHSDSQWYAA 114 ++ I + +L TY R +V+ HG+G ++D + K Y+D AAGIAV ALG+S+ + A Sbjct: 4 QEYIDTAEQELLHTYNRFSLVLDHGEGVYLYDTDKKAYLDFAAGIAVCALGYSNEAYKNA 63 Query: 115 LVEQAEKLAHTSNLYHTQPQVELAKRLVENSFADKAFFCNTGTEANEGAIKFARKWARVR 174 L +Q +KL HTSNLY+ P +E AK+ ++ S D+ FF N+GTEA EGAIK A+K+A R Sbjct: 64 LKDQVDKLLHTSNLYYNVPTIEAAKKALKASGMDRIFFTNSGTEAIEGAIKAAKKYAYTR 123 Query: 175 AGIDPYDGGAVAPYELVSFTSCFHGRTMGALALTYKEQYKTPFYPMMPGHQLAEYNNLES 234 G A +E+++ FHGR++GAL++T Y+ PF P+MPG + AEYNNLES Sbjct: 124 DG--------HAGHEIIAMKHSFHGRSIGALSVTGNAHYQEPFAPLMPGVKFAEYNNLES 175 Query: 235 AAAVIKKGKTAAVFVEPVQGEGGVTPSTQAFLKGLRQLCDEAGALLVFDEVQCGLGRTGK 294 ++ KT AV +E VQGEGG+ P+ AF++G+R+LCDE LL+ DE+QCG+GRTG+ Sbjct: 176 VKELV-TDKTCAVIMETVQGEGGIYPADPAFIEGVRRLCDEKDILLILDEIQCGMGRTGE 234 Query: 295 LWGHQLFGVEPDMMTLAKPLAGGLPIGTVLLKQHVAD-VMKPGDHGSTFAGNPLVCHVAC 353 ++ Q +GV+PD+MT AK L G+P+G L Q VAD + PGDHG+T+ GNP V Sbjct: 235 MFAWQNYGVKPDIMTCAKALGCGVPVGAFFLTQRVADKSLAPGDHGTTYGGNPFVGAAVS 294 Query: 354 SVFDIINSPAFLAAVEAKGERLRAGLRRTMAGNPHVQEVRGVGLLVGVQLDMMAGPVVDA 413 +VFD + L V+ L L + + RG GL+ GV + G V A Sbjct: 295 AVFDQFKACDILGHVKEVAPYLEQKLDELVEKYDFLITRRGKGLMQGVVCKLPVGKVAAA 354 Query: 414 ARDMGVMAITAGKGDVIRLVPPLVVTDAEIDTACEVLAAALNKV 457 A + G++ ITAG DV+R VPPLV+ +D E L AL V Sbjct: 355 ALEQGLIVITAG-ADVLRFVPPLVIEKQHVDEMIEKLEKALLSV 397 Lambda K H 0.319 0.134 0.396 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: 487 Number of extensions: 17 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: 460 Length of database: 399 Length adjustment: 32 Effective length of query: 428 Effective length of database: 367 Effective search space: 157076 Effective search space used: 157076 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