Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate SM_b21185 SM_b21185 succinate-semialdehyde dehydrogenase (NAD(P)+) protein
Query= BRENDA::P25526 (482 letters) >FitnessBrowser__Smeli:SM_b21185 Length = 491 Score = 569 bits (1466), Expect = e-167 Identities = 272/458 (59%), Positives = 349/458 (76%), Gaps = 1/458 (0%) Query: 25 GEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERATILRNWFNLMM 84 G DV+NP+ G+ L ++P MG D+ R AIDAA A P W AK+R+ ILR W +L++ Sbjct: 32 GPVFDVSNPSTGELLATLPDMGIDDARTAIDAAALAQPLWAGKPAKDRSIILRRWHDLIV 91 Query: 85 EHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGHQADKRLIVIK 144 EH DDLA ++T E GKP+ EAKGE+ +AAS++EW+AEE KR+YG+T P D+R++VIK Sbjct: 92 EHADDLAAILTAEMGKPVGEAKGEVLHAASYVEWYAEEAKRVYGETFPAPANDRRMLVIK 151 Query: 145 QPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAELAIRAGVPAG 204 QP+GV ITPWNFPA+M+ RK PALAAGCT+VLKPA QTP A A+ LA +AG P G Sbjct: 152 QPVGVVGTITPWNFPASMVARKISPALAAGCTIVLKPAEQTPLVAGAMFVLAEKAGFPEG 211 Query: 205 VFNVVTGSAGA-VGNELTSNPLVRKLSFTGSTEIGRQLMEQCAKDIKKVSLELGGNAPFI 263 V N++ S GA +G EL NP VRK+SFTGSTE+GR LM QC+ IKKVSLELGGNAPFI Sbjct: 212 VLNLLYASEGAPIGRELCGNPKVRKISFTGSTEVGRLLMRQCSDQIKKVSLELGGNAPFI 271 Query: 264 VFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAVSKLHIGDGLD 323 VFDDAD+D+AV+GA+ +KFRNAGQTCV ANR+YVQ V+D FAEK V +L +GDG Sbjct: 272 VFDDADIDEAVDGAVQAKFRNAGQTCVSANRIYVQSAVHDAFAEKFVTRVRELTVGDGFA 331 Query: 324 NGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGGNFFQPTILVDVPANAKVS 383 V IGP+ID A+ K+E H+ADA+ KGA+V GG G FF+PT+L + + +++ Sbjct: 332 PDVAIGPMIDAHAIDKIEAHVADAVAKGAQVRSGGSRIGTTGTFFEPTVLTGISHDMRIA 391 Query: 384 KEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEALEYGIVGINTG 443 +EETFGP+AP+ RF+ V+A+ANDT +GLAAYFYA +L RV+ V EALEYG+VGINTG Sbjct: 392 QEETFGPIAPIIRFETAEQVVAEANDTIYGLAAYFYAENLKRVWHVAEALEYGMVGINTG 451 Query: 444 IISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481 +S+E APFGGIK SG+GREGS++G+EDYLE+KY+C+G Sbjct: 452 RMSSEAAPFGGIKQSGIGREGSRHGLEDYLEMKYLCMG 489 Lambda K H 0.318 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: 709 Number of extensions: 29 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: 482 Length of database: 491 Length adjustment: 34 Effective length of query: 448 Effective length of database: 457 Effective search space: 204736 Effective search space used: 204736 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