Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_012674835.1 SULAZ_RS03325 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000021545.1:WP_012674835.1 Length = 386 Score = 322 bits (824), Expect = 1e-92 Identities = 170/375 (45%), Positives = 245/375 (65%), Gaps = 10/375 (2%) Query: 9 YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68 Y R FE+GEG YLY G+++LD +G+AVN LG+ +P L +A+ QA K+ H SNL Sbjct: 13 YGRLPYFFEKGEGCYLYDDKGKKYLDMLSGIAVNALGYNHPKLTKAICEQASKIIHISNL 72 Query: 69 FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQA 128 F + Q +AK L+E +F VFF NSGAE+ E KL+R+Y Y+K + R IITFE + Sbjct: 73 FYIKPQIEVAKILSENSFGGKVFFCNSGAESNEALIKLVRRYFYDKKQE-RYEIITFEGS 131 Query: 129 FHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEGG 188 FHGRTLA V+A Q K +GF PL++GF F D+++V+N +TD+TA I +E +QGEGG Sbjct: 132 FHGRTLATVTATAQPKYHEGFYPLVEGFKYAKFNDIDSVKNLITDKTAAILIELVQGEGG 191 Query: 189 IRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGGG 248 + + EF++ L ++C E+ +L +DE+Q G+GRTGKLFA++ I PD++++AKG+GGG Sbjct: 192 VNPANKEFIKELYKLCKENDILFTVDEVQTGIGRTGKLFAYQHFDIQPDIISLAKGLGGG 251 Query: 249 FPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQD 308 P+GA +A + A GTH ST+GGN L+T VL++VL GFLD VQ++G L++ Sbjct: 252 VPIGAIIAKDDIAKSFVPGTHASTFGGNYLSTVAAKVVLEEVLSEGFLDRVQKVGEYLKE 311 Query: 309 RLAGLVAENPAVFKGVRGKGLMLGLACGPAVG--DVVVALRANGLLSVPAGDNVVRLLPP 366 L + P V+G GLM+G+ ++ +V+ GL+ AG+N +R +PP Sbjct: 312 ALK--IFGYP-----VKGLGLMVGMDLPQSISAKEVMKKTLEKGLIVGTAGENTLRFVPP 364 Query: 367 LNIGEAEVEEAVAIL 381 L I E EV+EAV IL Sbjct: 365 LIITEKEVDEAVDIL 379 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: 381 Number of extensions: 17 Number of successful extensions: 3 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: 386 Length adjustment: 30 Effective length of query: 359 Effective length of database: 356 Effective search space: 127804 Effective search space used: 127804 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 Jul 25 2024. The underlying query database was built on Jul 25 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