Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_015944558.1 DHAF_RS16705 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::B1A0U3 (469 letters) >NCBI__GCF_000021925.1:WP_015944558.1 Length = 430 Score = 139 bits (351), Expect = 1e-37 Identities = 101/321 (31%), Positives = 154/321 (47%), Gaps = 23/321 (7%) Query: 52 PIVFAHAKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFYND 111 PI A +G+ +WD +GN Y+D++ + + GH HP ++ A+ A+R T S A Sbjct: 37 PIFIAKGQGARLWDIDGNSYLDYVLSWGPLILGHAHPVVVGAIKAAAERGT-SYGAPTEI 95 Query: 112 RFPVFAEYLTALFGYDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVSCCGCFN 171 E + A +MV +++G E +AL+LAR K I+ GC++ Sbjct: 96 ETECAEEVIKAFPSMEMVRMVSSGTEATMSALRLARGVTGRNK--------IIKFEGCYH 147 Query: 172 GRTLGVISMSCDNEATRGFGPLMPG--------HLKVDFGDAEAIERIFKEKGDRVAAFI 223 G ++ + T G P PG + + D E ++ IFKE G+ +AA I Sbjct: 148 GHGDSLLIKAGSGALTFGV-PTSPGVPSSVASQTIVAQYNDLEGLKEIFKECGEDIAAVI 206 Query: 224 LEPIQGEAGVVIPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVV 283 LEP+ G GVV+P G+L +R L Y L+I DE+ TG R A + PD+ Sbjct: 207 LEPVTGNMGVVLPQPGFLAGLRTLTQDYGSLLIFDEVMTGF-RVSYGGAQGRYQIDPDLT 265 Query: 284 ILGKALGGGILPVSAVLADKDVMLCIKPG---QHGSTFGGNPLASAVAIAALEVIKEERL 340 LGK +GGG LPV+A + M + P T GNPLA A +A L+++++E + Sbjct: 266 CLGKVIGGG-LPVAAYGGKRKYMEQVAPSGPIYQAGTLSGNPLAMAAGLATLKLLQQEGV 324 Query: 341 TERSTKLGGELLGLLHKIQKK 361 E K L L I ++ Sbjct: 325 YEGLEKKTARLAEGLQSIAQE 345 Lambda K H 0.319 0.137 0.409 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: 433 Number of extensions: 24 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: 469 Length of database: 430 Length adjustment: 33 Effective length of query: 436 Effective length of database: 397 Effective search space: 173092 Effective search space used: 173092 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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