Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 16426 b2319 hypothetical protein (NCBI)
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Keio:16426 Length = 337 Score = 310 bits (793), Expect = 4e-89 Identities = 161/337 (47%), Positives = 218/337 (64%), Gaps = 3/337 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 MS+ +N+A+ GATGAVGE +LE L ER+FPV E++ LA S G+ RF GKT+ VQ+ Sbjct: 1 MSEGWNIAVLGATGAVGEALLETLAERQFPVGEIYALARNESAGEQLRFGGKTITVQDAA 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 EFDW+Q +A F AG E +A W A +G +VID++ F + D+PLVVPEVNP + + Sbjct: 61 EFDWTQAQLAFFVAGKEATAAWVEEATNSGCLVIDSSGLFALEPDVPLVVPEVNPFVLTD 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 +RNRN+IA P+ T Q+L ALKP+ D G+ RI+VT+ S S GK +D LAGQ+AKLL Sbjct: 121 YRNRNVIAVPDSLTSQLLAALKPLIDQGGLSRISVTSLISASAQGKKAVDALAGQSAKLL 180 Query: 181 NGYPA-ETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRV 239 NG P E + F +Q+AFN +P + G +EE ++V E +KI D +M++ + V+ Sbjct: 181 NGIPIDEEDFFGRQLAFNMLPLLPD--SEGSVREERRIVDEVRKILQDEGLMISASVVQA 238 Query: 240 PVFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVR 299 PVFYGHA+ V+ E P+ AE+ D Q + I L +FPTQV DA G H+ VG VR Sbjct: 239 PVFYGHAQMVNFEALRPLAAEEARDAFVQGEDIVLSEENEFPTQVGDASGTPHLSVGCVR 298 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 ND + W VADNVR G A AV+IAE LV++Y Sbjct: 299 NDYGMPEQVQFWSVADNVRFGGALMAVKIAEKLVQEY 335 Lambda K H 0.319 0.135 0.395 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: 299 Number of extensions: 8 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: 337 Length of database: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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: 49 (23.5 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