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) >FitnessBrowser__Smeli:SM_b21185 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:
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