Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate SM_b21185 SM_b21185 succinate-semialdehyde dehydrogenase (NAD(P)+) protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >lcl|FitnessBrowser__Smeli:SM_b21185 SM_b21185 succinate-semialdehyde dehydrogenase (NAD(P)+) protein Length = 491 Score = 561 bits (1446), Expect = e-164 Identities = 267/458 (58%), Positives = 352/458 (76%), Gaps = 3/458 (0%) Query: 25 GQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERATKLRRWYELII 84 G V+NP+TGE+L T+P MG + R AI+AA A P W AK+R+ LRRW++LI+ Sbjct: 32 GPVFDVSNPSTGELLATLPDMGIDDARTAIDAAALAQPLWAGKPAKDRSIILRRWHDLIV 91 Query: 85 ENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPGHQPDKRLIVIK 144 E+ DDLA ++T E GKP+ EAKGE+++AAS++EW+AEEAKR+YG+ P D+R++VIK Sbjct: 92 EHADDLAAILTAEMGKPVGEAKGEVLHAASYVEWYAEEAKRVYGETFPAPANDRRMLVIK 151 Query: 145 QPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFALAELAQRAGIPAG 204 QP+GV ITPWNFPA+M+ RK PALAAGCT+VLKPA QTP A A+ LA++AG P G Sbjct: 152 QPVGVVGTITPWNFPASMVARKISPALAAGCTIVLKPAEQTPLVAGAMFVLAEKAGFPEG 211 Query: 205 VFSVVSGSAG-DIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKVSLELGGNAPFI 263 V +++ S G IG EL NP VRK+SFTGSTE+GR LM +C+ IKKVSLELGGNAPFI Sbjct: 212 VLNLLYASEGAPIGRELCGNPKVRKISFTGSTEVGRLLMRQCSDQIKKVSLELGGNAPFI 271 Query: 264 VFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVAVAKLKIGNGLE 323 VFDDAD+D+AV+GA+ +K+RN GQTCV ANR+Y+Q V+DAFAEK V +L +G+G Sbjct: 272 VFDDADIDEAVDGAVQAKFRNAGQTCVSANRIYVQSAVHDAFAEKFVTRVRELTVGDGFA 331 Query: 324 AGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFEPTILTNVPNNAAVA 381 GP+ID A+ K++ H+ADA++KGA V +GG + G FFEPT+LT + ++ +A Sbjct: 332 PDVAIGPMIDAHAIDKIEAHVADAVAKGAQVRSGGSRIGTTGTFFEPTVLTGISHDMRIA 391 Query: 382 KEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGVNTG 441 +EETFGP+AP+ RF+ V+A +NDT +GLA+YFYA +L RV+ VAEALEYGMVG+NTG Sbjct: 392 QEETFGPIAPIIRFETAEQVVAEANDTIYGLAAYFYAENLKRVWHVAEALEYGMVGINTG 451 Query: 442 LISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479 +S+E APFGGIK SG+GREGS++G+EDYLE+KYLC+G Sbjct: 452 RMSSEAAPFGGIKQSGIGREGSRHGLEDYLEMKYLCMG 489 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: 671 Number of extensions: 25 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: 480 Length of database: 491 Length adjustment: 34 Effective length of query: 446 Effective length of database: 457 Effective search space: 203822 Effective search space used: 203822 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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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