Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_084201012.1 C0029_RS15270 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::Q9FNK4 (475 letters) >NCBI__GCF_002869505.1:WP_084201012.1 Length = 426 Score = 134 bits (336), Expect = 8e-36 Identities = 94/302 (31%), Positives = 151/302 (50%), Gaps = 23/302 (7%) Query: 59 PVVFSRANGSTIWDPEGKRYIDFLAAYSAVNQGHCHPKIMKALQEQVEKLTLSSRAFYND 118 PV R++G+ ++D EGK YID++ ++ + GH HP + +A+ +Q EK LS A Sbjct: 33 PVFIDRSDGARVYDCEGKAYIDYVLSWGPMIMGHNHPAVREAVIKQSEK-GLSFGAPTEL 91 Query: 119 KFPVFAERLTNMFGYDMVLPMNTGAEGVETALKLARKWGHEKKNIPKDEAIIVSCCGCFH 178 + + M G D+V +N+G E +A++LAR G+ ++ IV GC+H Sbjct: 92 EIQLADRICEIMPGMDLVRMVNSGTEATMSAIRLAR--GYTGRDT------IVKFEGCYH 143 Query: 179 GRTLAIVSMSCDNDATRGFGPLLPG--------NLKVDFGDADSLEKIFKEKGDRIAGFL 230 G + +++ + T G P PG + + + D + + F E GD IA + Sbjct: 144 GHSDSLLVKAGSGALTMGV-PSSPGVPAALADHTMTLTYNDPEGVRAAFAEHGDSIACVI 202 Query: 231 FEPIQGEAGVIIPPDGYLKAVRELCTKYNVLMIADEVQSGLARSGKMLACDWEEIRPDMV 290 EP+ G I P G+L+ +RE C ++I DEV +G R G A + + D+ Sbjct: 203 VEPVAGNMNCIPPEPGFLETLRECCDVSGAVLILDEVMTGF-RFGLQGAQGFFGVEADLT 261 Query: 291 ILGKALGGGVIPVSAVLADKDVMLHIK---PGQHGSTFGGNPLASAVAMASLDVIVEEKL 347 LGK +GGG +PV A +++M I P T GNP+A A +A+LD+I + Sbjct: 262 TLGKVVGGG-MPVGAFGGKREIMEQIAPLGPVYQAGTLSGNPIAMAAGLATLDIISADGF 320 Query: 348 VE 349 E Sbjct: 321 YE 322 Lambda K H 0.318 0.136 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: 482 Number of extensions: 17 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: 475 Length of database: 426 Length adjustment: 33 Effective length of query: 442 Effective length of database: 393 Effective search space: 173706 Effective search space used: 173706 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 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