Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate Echvi_2301 Echvi_2301 amino acid adenylation domain
Query= reanno::Cola:Echvi_3848 (381 letters) >FitnessBrowser__Cola:Echvi_2301 Length = 2214 Score = 87.4 bits (215), Expect = 4e-21 Identities = 84/296 (28%), Positives = 127/296 (42%), Gaps = 31/296 (10%) Query: 16 KASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYSNSVQIPIQKEL 75 ++ GS IWD GNEYLD+ G I GH + +KEQ++ Y Q + + Sbjct: 1767 RSKGSRIWDIDGNEYLDILNGFGSILFGHKPDFIDEALKEQIEK--GYEIGPQHELSGAV 1824 Query: 76 ATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHG-----RTSGA 130 + ++G+ LCN+G+EA AL++A T + +AF +HG G Sbjct: 1825 CKLICDITGHD--RAALCNTGSEAVMGALRIARTITQRSLVVAFNGSYHGIFDEVIVRGT 1882 Query: 131 VALTDNPKIIAPF-NAHEGVHILPFNDLEAVE-KQLATGTIAGVIVEGIQGVGGIQVPDP 188 +L P + E + IL + E + + IA V+VE +Q + Sbjct: 1883 KSLKSFPAAAGIMAESVENILILDYGTAETLRIIEERKDEIAAVLVEPVQS-RRPEFQPV 1941 Query: 189 AFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGNGFPIGG 248 FL + +T G+ LI DEV +G+ + Q + G+K DL T K +G G PIG Sbjct: 1942 DFLKKVREITAAVGSALIFDEVITGFRMHPQ--GAQGIFGIKADLATYGKVVGGGLPIGV 1999 Query: 249 VLISPEF----KASHGLLGT-------------TFGGNHLACAAALAVLEVIDEEN 287 + EF H G TF + LA A A A LE I +++ Sbjct: 2000 IAGKAEFMDALDGGHWQYGDASVPEIDVTYFAGTFVRHPLALATAKASLEYIQQDD 2055 Lambda K H 0.318 0.137 0.400 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: 1712 Number of extensions: 77 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: 381 Length of database: 2214 Length adjustment: 43 Effective length of query: 338 Effective length of database: 2171 Effective search space: 733798 Effective search space used: 733798 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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