Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_012276110.1 SHAL_RS05025 aspartate aminotransferase family protein
Query= BRENDA::Q6LFH8 (414 letters) >NCBI__GCF_000019185.1:WP_012276110.1 Length = 446 Score = 126 bits (317), Expect = 1e-33 Identities = 107/416 (25%), Positives = 172/416 (41%), Gaps = 40/416 (9%) Query: 29 PVVLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFSD 88 P +L +G++ D+ R D + N GH +I A+ Q ++ Sbjct: 32 PRMLAHAEGMYYKDVAGRPILDGTAGLWCCNAGHGRKEISEAVSKQIHEMDYAPSFQMGH 91 Query: 89 SLGV-CERYLTNLF--GYDKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCNN 145 L L + G +KV N+G+E+ ++A K+ Y + I Sbjct: 92 PLAFELAGRLAQISPEGLNKVFFTNSGSESVDSALKIALT--YHRANGEATRTRFIGREL 149 Query: 146 NFSGRTLGCVSASTDKKCKNNFGP-------------------FVPNFLKVPYDDLEALE 186 + G G +S + F F K + E LE Sbjct: 150 GYHGVGFGGISVGGIGNNRKTFNQQLLQGVDHLPHTLDMKDNAFCRGMPKTGAEKAEVLE 209 Query: 187 KELQ---DPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTG 243 + + N+ A IVEP+ G AGVI+P + Y + + KY +L + DEV T GR G Sbjct: 210 QLVALHGAENIAAVIVEPMSGSAGVILPPEGYLQKLREITTKYGILLIFDEVITAFGRVG 269 Query: 244 KLLCTHHYGVKPDVILLGKALSGGHYPISAILANDDVMLVLKPGE-------HGSTYGGN 296 + +GV PD+I KAL+ G P+ A+L +D + G HG TY G+ Sbjct: 270 DAFASQRWGVVPDMITTAKALNNGAIPMGAVLVDDKIYDTCMQGPENAIELFHGYTYSGH 329 Query: 297 PLAAAICVEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIEFKN 356 P+AAA + L + NEKL E +L + ++ LK V ++R GL+ I+F Sbjct: 330 PVAAAAALATLNIYENEKLFERTKELEG-YFEDAVHSLKGLPNVIDIRNTGLVGGIQFAP 388 Query: 357 DLVNV----WDICLKFKENGLITRSVHDKTVRLTPPLCITKEQLDECTEIIVKTVK 408 V + I E G + R+ D + ++PPL + K+Q+D+ + +K Sbjct: 389 SEQGVGKRGFGIFEHCFEAGTLVRATGD-IIAISPPLIVDKQQIDQIVNTLGDAIK 443 Lambda K H 0.320 0.138 0.418 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: 401 Number of extensions: 20 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: 414 Length of database: 446 Length adjustment: 32 Effective length of query: 382 Effective length of database: 414 Effective search space: 158148 Effective search space used: 158148 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