Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF3251 PGA1_c33040 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Phaeo:GFF3251 Length = 479 Score = 324 bits (831), Expect = 4e-93 Identities = 178/472 (37%), Positives = 272/472 (57%), Gaps = 11/472 (2%) Query: 10 RQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTA 69 ++ +I+G WV +V +P+T + AA+T A+ AA ALP W Sbjct: 4 KRDFYINGQWVAPAAPNDFEVIDPSTEAPCAVISLGDAADTNAAVAAAKTALPGWMTTPV 63 Query: 70 KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASF-IEWFAEEAKRIYG 128 +ER + + E+ +DLA+ M++E G P+ A+ + A S+ + F + AK Sbjct: 64 EERIALVEKLIEVYESRTEDLAQAMSVEMGAPIDMARTQQAGAGSWHLRNFIKAAKAFSF 123 Query: 129 DVIPG-HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPF 187 D G H P+ R +I + +GV A ITPWN+P +T K G A AGCTMVLKP+ Q+P Sbjct: 124 DAPLGDHAPNDR--IIHEAVGVAALITPWNWPMNQVTLKVGAAAIAGCTMVLKPSEQSPL 181 Query: 188 SAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK 247 +A AE+ AG PAGVF++V+G +G++L+S+P V +SFTGST G + A Sbjct: 182 NAMIFAEMMDEAGFPAGVFNLVNGDGTGVGTQLSSHPDVDMVSFTGSTRAGTAISKAAAD 241 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307 +KKV LELGG ++FDDAD +KAV+ ++ N GQ+C +R+ +Q G+YD E Sbjct: 242 TLKKVHLELGGKGANVIFDDAD-EKAVKRGVLHMMNNTGQSCNAPSRMLVQKGIYDKAVE 300 Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAG--GKP---ME 362 + K+++G G GP+++E K+Q+ I + +GA ++AG G+P + Sbjct: 301 EAAAVANKVEVGPASSEGRHIGPVVNELQWGKIQDLIQKGIDEGARLVAGGTGRPDGLNQ 360 Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422 G + +PT+ +V N +A+EE FGP+ + F+ E D I ++NDT +GL +Y +DL Sbjct: 361 GFYVKPTVFADVNNQMTIAREEIFGPVLSIIPFESEEDAIEIANDTPYGLTNYVQTQDLA 420 Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 R R+A L GM+ +N G + +PFGG+K SG GREG +GIED+LE+K Sbjct: 421 RANRMARKLRAGMIEMN-GKSRSAGSPFGGMKQSGNGREGGSWGIEDFLEVK 471 Lambda K H 0.317 0.135 0.390 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: 583 Number of extensions: 24 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: 480 Length of database: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 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 17 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