Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012043307.1 BBTA_RS14845 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::L7N4M1 (449 letters) >NCBI__GCF_000015165.1:WP_012043307.1 Length = 431 Score = 468 bits (1203), Expect = e-136 Identities = 236/424 (55%), Positives = 301/424 (70%), Gaps = 3/424 (0%) Query: 17 SFETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTD 76 +FET +HAGQ PDP T ARA+PIY TTSY FDDT HAAALF LE G+IYTRI NPTT Sbjct: 8 AFETLSLHAGQQPDPATGARAVPIYQTTSYVFDDTEHAAALFNLERAGHIYTRISNPTTA 67 Query: 77 VVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKL 136 V+E+R+AALEGGV A+ +SGQAA AI L AGDHIV+S LYGGT NL ++L + Sbjct: 68 VLEERLAALEGGVGAICTASGQAALHLAIATLLNAGDHIVASSSLYGGTINLLAHTLPRF 127 Query: 137 GIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDN 196 GI SFV P DLD ++AA++P TK ET+ NP +++LD P +S +AH G+PL++DN Sbjct: 128 GITTSFVK-PRDLDGFRAAIQPKTKLVIGETLGNPGLEVLDIPRISAIAHEAGIPLLIDN 186 Query: 197 TIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW-TQGRFPGFTTPDPS 255 T ATPYL QP+AQGADIV+HSATK+LGGHG AI G I+DGG FDW G+FP T P Sbjct: 187 TFATPYLSQPIAQGADIVMHSATKWLGGHGIAIGGAIIDGGRFDWRASGKFPQLTEPYAG 246 Query: 256 YHGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRV 314 YHG+VF E GP AF ++AR + LRD+G+ SP NAF + QG+ETL LR+ERHVAN V Sbjct: 247 YHGIVFDEQFGPAAFIMRARTEGLRDFGACLSPTNAFHLLQGVETLHLRMERHVANTSAV 306 Query: 315 AEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKLH 374 L A V V + L + P H AK+L P+G G+++SF + GG AG+ F+ +LKL Sbjct: 307 LAALTANKAVDWVLHPSLETHPDHALAKQLLPRGAGSIISFGIKGGRPAGRKFIESLKLI 366 Query: 375 SHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGFA 434 SH+AN+GD ++LVIHPASTTH Q+ A+ A G+ L+RL+VGIE + DI+ DL Sbjct: 367 SHLANVGDAKTLVIHPASTTHQQMDAAQLAAAGIGEELIRLSVGIEAVSDIIDDLGQALR 426 Query: 435 AARR 438 A+++ Sbjct: 427 ASQK 430 Lambda K H 0.318 0.134 0.394 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: 605 Number of extensions: 25 Number of successful extensions: 4 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: 449 Length of database: 431 Length adjustment: 32 Effective length of query: 417 Effective length of database: 399 Effective search space: 166383 Effective search space used: 166383 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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