Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_084704226.1 BS73_RS20475 hypothetical protein
Query= BRENDA::Q8KQ27 (354 letters) >NCBI__GCF_000744815.1:WP_084704226.1 Length = 432 Score = 340 bits (873), Expect = 3e-98 Identities = 186/378 (49%), Positives = 239/378 (63%), Gaps = 29/378 (7%) Query: 3 PVLALVGATGAVGTVMIDIINNRETVPWGEIRLIASARSAGKKLTVRGEELTVIELTAEA 62 P L + GATG +G+V++++++ R V WGEIRL A+ G++LTVRGEE + L + Sbjct: 43 PTLVVAGATGRIGSVLLELLSTRSDV-WGEIRLAAAPEEHGRRLTVRGEETELRALDEDC 101 Query: 63 FDGVDVAMFDVPDEISAEWAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNADKVGERPR 122 F G D+A+F +P ++A WAP+A G V VD+SGAFRM +VPLVVPEVNA RPR Sbjct: 102 FAGADIALFALPKPLAARWAPIAVGNGCVVVDSSGAFRMHPEVPLVVPEVNAATARLRPR 161 Query: 123 GIIANPNCTTLSMMAALGALHREFELKELVVASYQAVSGAGKEGVDRLYAELEAV----- 177 G++A P TT + ALGALH EF L ELV+A+YQA SGAG+ GV RL A+L AV Sbjct: 162 GVVAGPRGTTPPLAVALGALHAEFGLAELVLATYQAASGAGESGVRRLRAQLSAVAVGQA 221 Query: 178 AGKPVGVSAGDVRKTL-----------------EAAGLSISDSPFP------APLAFNVV 214 AG+ G GDVR+ + EAAG + + P APLA NVV Sbjct: 222 AGQAPGTYPGDVRRAIGDLDEHGEPLRPEASGPEAAGAEAAGAEAPGADPDDAPLALNVV 281 Query: 215 PSAGSYKGDGWYSEELKVRNESRKILGIPDLKVSATCVRVPVVTTHSLAVHATFAREVTV 274 P G + DGW SEEL +R E RKILG+P+LK +ATCVRVPVVT HS+AVHA FAREVTV Sbjct: 282 PWCGRTEEDGWSSEELGLREELRKILGLPELKATATCVRVPVVTGHSIAVHAVFAREVTV 341 Query: 275 EEAHKVFEAQPTIVLVDDPENGVFPTPAEVVGEDPTYVGRVRQALDFPNTLDFLRVRGQP 334 E AH+V P +++ DDPE FPTP +VVG DP +VGRVR++ D P LDF Sbjct: 342 ERAHRVLAEAPGVLVYDDPEQREFPTPVDVVGTDPAWVGRVRRSPDDPRALDFFLCADNL 401 Query: 335 AQGAAAEHLRDAETLAPQ 352 +G A ++ AE + + Sbjct: 402 RKGGALNLVQIAEAVCAE 419 Lambda K H 0.316 0.133 0.381 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: 473 Number of extensions: 17 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: 354 Length of database: 432 Length adjustment: 31 Effective length of query: 323 Effective length of database: 401 Effective search space: 129523 Effective search space used: 129523 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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