Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_085217210.1 B9N75_RS01575 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_900177405.1:WP_085217210.1 Length = 396 Score = 410 bits (1054), Expect = e-119 Identities = 207/383 (54%), Positives = 268/383 (69%) Query: 5 VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64 +MP Y R+ + RGEG YLY G +LDFA+G+AVN+LGH +P+L +A+ QA L H Sbjct: 6 LMPVYPRSPVRPVRGEGCYLYGEGGETYLDFASGIAVNLLGHGHPHLTKAIQDQAATLIH 65 Query: 65 TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124 SNL+ E+LA+RL ++TFADTVFFTNSGAEA EC K R+YH+ G + +IT Sbjct: 66 VSNLYGSPQGEALAQRLVDSTFADTVFFTNSGAEAVECAIKTARRYHHHHGRPEKHTLIT 125 Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQ 184 F+ AFHGRTL +SA Q KL GF PLL GF + F +L+A + A+ D TAG +EP+Q Sbjct: 126 FKNAFHGRTLGTISATDQAKLRDGFAPLLPGFTVAEFDNLDAAKAAIDDHTAGFLVEPVQ 185 Query: 185 GEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKG 244 GEGGIR S EF++GLR + DEH L+L LDE+QCG+ RTGKL+A+E GI PD++A AKG Sbjct: 186 GEGGIRPASQEFMKGLRALADEHDLMLVLDEVQCGVARTGKLYAYEHYGIEPDILASAKG 245 Query: 245 IGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGG 304 IGGGFP+GACLATEKAA+GM GTHGSTYGG PLA A G AVLD V P FL+ V R+G Sbjct: 246 IGGGFPMGACLATEKAAAGMVIGTHGSTYGGGPLAMAAGGAVLDVVNTPEFLERVTRMGD 305 Query: 305 LLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLL 364 L+ L ++ + +F+ VRG GLMLG+ V LR +GLL+V AGDNV+R+L Sbjct: 306 RLRGALEQMIPNHDHLFESVRGLGLMLGIKMKTDSRAFVTYLRDHGLLTVAAGDNVMRVL 365 Query: 365 PPLNIGEAEVEEAVAILAKTAKE 387 PPL I ++ + E V L++ A++ Sbjct: 366 PPLVIEDSHIAEFVEKLSEAARQ 388 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: 496 Number of extensions: 16 Number of successful extensions: 1 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: 396 Length adjustment: 31 Effective length of query: 358 Effective length of database: 365 Effective search space: 130670 Effective search space used: 130670 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 26 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