Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 246 bits (627), Expect = 1e-69 Identities = 144/375 (38%), Positives = 208/375 (55%), Gaps = 24/375 (6%) Query: 12 RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEM 71 RG G VWD +GR Y+D GI V LGHAHPE + + Q K+ G + ++ + Sbjct: 28 RGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHIGNGYTNEPVLRL 87 Query: 72 LEELSHWVDYEYVYMGNSGTEAVEAAIKFARLAT------GRSEIVAMTNAFHGRTLGSL 125 + L + + NSG EA EAA+K AR + EI++ T +FHGRT ++ Sbjct: 88 AKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRHGADKYEIISFTQSFHGRTFFTV 147 Query: 126 SATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEFV 185 S + KY EGFGP+ G H+P+N++EA K+AI +T AVI EPIQGEGG++PAD F+ Sbjct: 148 SVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQTCAVIVEPIQGEGGVIPADPAFL 207 Query: 186 KTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLTD 244 K LR+ + GALLI DEVQ+G+ R+G F A + GV PDI+T K +GNGFP+ LT Sbjct: 208 KALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVTPDILTTAKALGNGFPIGAMLTT 267 Query: 245 LEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSG------ER- 293 E+ G HG+T+GGNPL + ++ +L+E + G ER Sbjct: 268 NELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKLLEGVRSRSEALKGHLAKLNERF 327 Query: 294 --VVKTRGRGLMIGIVLRRP----AGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTL 347 + RGRGL+IG L A ++V A + G+++ AG V+R +P LI+ D + Sbjct: 328 GLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVIMLMAGPDVLRFVPSLIMPLDDM 387 Query: 348 EEARKEIEGVLNDIL 362 E + + + I+ Sbjct: 388 NEGFERLAKAIESIV 402 Lambda K H 0.320 0.140 0.410 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: 376 Number of extensions: 21 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: 362 Length of database: 411 Length adjustment: 30 Effective length of query: 332 Effective length of database: 381 Effective search space: 126492 Effective search space used: 126492 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: 50 (23.9 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