Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate PP_0372 PP_0372 Acetylornithine aminotransferase 2
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__Putida:PP_0372 Length = 426 Score = 234 bits (598), Expect = 3e-66 Identities = 159/386 (41%), Positives = 207/386 (53%), Gaps = 8/386 (2%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +MP RA VF RG+G +L+ +G +LDF G AVN LGH+ LV+AL QA L + Sbjct: 35 LMPGTERAAQVFVRGQGSWLWDNEGHAYLDFTQGGAVNSLGHSPSVLVKALGNQAQALIN 94 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 + F G L RL ++T +D + NSGAEA E KL RK+ + A IIT Sbjct: 95 PGSGFHNRGLLGLVNRLCQSTGSDQAYLLNSGAEACEGAIKLARKWGQLHRNGAY-HIIT 153 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 QA HGR+L A+SA+ + P L GF VPF DL A+ V T I LEPIQ Sbjct: 154 ASQACHGRSLGALSASDPLPCNR-CEPGLPGFSKVPFNDLAALHAEVDSRTVAIMLEPIQ 212 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GE G+ + E+L+G+ +C E G+LL LDE+Q G+GR G L A E G+ D++ + KG Sbjct: 213 GEAGVIPATQEYLKGVETLCRELGILLILDEVQTGIGRCGALLAEELYGVRADIITLGKG 272 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 +GGG PL A LA KA GS + GN L A G AVLD VLEPGFL VQ G Sbjct: 273 LGGGVPLAALLARGKACCAEPGELEGS-HHGNALMCAAGLAVLDSVLEPGFLAQVQDNGR 331 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGD--VVVALRANGLLSVPAGDNVVR 362 L++ L+ L VRG GL+ L + V AL LL+ P D VVR Sbjct: 332 HLREGLSRLTGRYGQ--GEVRGHGLLWALQLKENLARELVAAALHEGLLLNAPQVD-VVR 388 Query: 363 LLPPLNIGEAEVEEAVAILAKTAKEL 388 P L + + ++E + LA+ L Sbjct: 389 FSPALTVSKGNIDEMLLRLARAFARL 414 Lambda K H 0.321 0.139 0.414 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: 454 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: 389 Length of database: 426 Length adjustment: 31 Effective length of query: 358 Effective length of database: 395 Effective search space: 141410 Effective search space used: 141410 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