Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate PP_1992 PP_1992 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Putida:PP_1992 Length = 334 Score = 250 bits (638), Expect = 4e-71 Identities = 134/334 (40%), Positives = 201/334 (60%), Gaps = 3/334 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 M+ ++A+ GATG+VGE ++++L+E FPV L LLAS S G + F GK ++V+ V+ Sbjct: 1 MTHPLDIAVVGATGSVGEALVQILEELAFPVATLHLLASMESAGSSVMFAGKKLKVREVD 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 FD++QV +A F+ G +S +A A +AG VID + D +VPE N E +A Sbjct: 61 SFDFAQVKLAFFATGAAVSRSFAGKALQAGCTVIDLSGGLD---DALALVPEANAERLAS 117 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 I +P + + + VAL P+ + IER+ V +VS G+ + ELA QTA+LL Sbjct: 118 LSLPARIVSPCSAAVALAVALAPLKGLLDIERVQVMAALAVSAQGREAVSELARQTAELL 177 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 N P E F +Q+AFN + Q+ + G+T E ++V E + + P + ++ +CV+VP Sbjct: 178 NARPLEPRFFDRQVAFNLLAQVGAADEQGHTALERRLVSELRVLLGLPELKISVSCVQVP 237 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVRN 300 VF+G + +V V++R P+D V LE D IE D+PT V DA G+D V VGRVR+ Sbjct: 238 VFFGDSFSVAVQSRRPVDLAAVNQALEAADSIERVENDDYPTPVGDAVGQDVVYVGRVRH 297 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334 + +NLW+ DNVRKGAA NAVQ+A+LL++ Sbjct: 298 GVDEDQQLNLWLTTDNVRKGAALNAVQVAQLLIK 331 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: 239 Number of extensions: 9 Number of successful extensions: 2 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: 334 Length adjustment: 28 Effective length of query: 309 Effective length of database: 306 Effective search space: 94554 Effective search space used: 94554 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 Aug 03 2021. The underlying query database was built on Aug 03 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