Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_086511774.1 BZY95_RS20670 aldehyde dehydrogenase
Query= BRENDA::P30038 (563 letters) >NCBI__GCF_002151265.1:WP_086511774.1 Length = 486 Score = 138 bits (348), Expect = 4e-37 Identities = 140/476 (29%), Positives = 214/476 (44%), Gaps = 29/476 (6%) Query: 67 VVGDEEVWTSDVQYQVSPFNHGHKVAKFCYADKSLLNKAIEAALAARK----EWDLKPIA 122 ++G E V T + +P + G +A+ + A++AA A EW Sbjct: 13 LIGGEWVPTQALLDVQTP-SSGRTIAQIARCQAEEVMVAVDAARRAFAGSLGEWARWSAK 71 Query: 123 DRAQIFLKAADMLSGPRRAEILAKTMVGQGKTVIQAEIDAAAELIDFFRFNAKYAVELEG 182 R + L+ D + A + A GK + QAE D A +FRF A +L G Sbjct: 72 RRGEWLLQFGDAIDADH-ANLAALECADTGKPMSQAEADIRA-CARYFRFYGGGADKLHG 129 Query: 183 QQPISVPPSTNSTVYRGLE--GFVAAISPFNFTA-IGGNLAGAPALMGNVVLWKPSDTAM 239 + ++P TV E G A I P+N+ A I G A GN V+ KP++ A Sbjct: 130 E---TLPFDEGFTVLTLREPYGVCAQIIPWNYPAQIFGRCVAAALATGNSVVLKPAEDAC 186 Query: 240 LASYAVYRILREAGLPPNIIQFVPADGPLFGDTVTSSEHLCGINFTGSVPTFKHLWKQVA 299 L+ + + EAGLPP ++ VP G G + + + ++FTGS T QVA Sbjct: 187 LSVLRLAELACEAGLPPGVLNVVPGLGREAGAALAAHPAIDHLSFTGSPET----GTQVA 242 Query: 300 QNLDRFHTFPRLAGECGGKNFHFVHRSADVESVVSGTLRSAFEYGGQKCSACSRLYVPHS 359 Q H L E GGK+ V AD++ + +R+ + GQ CSA SRL V S Sbjct: 243 QAAAAHHVPVTL--ELGGKSPQIVFADADMDVALDAVVRAIIQNAGQTCSAGSRLLVEAS 300 Query: 360 LWPQIKGRLLEEHS--RIKVGDPAEDFGTFFSAVIDAKSFARIKKWLEHARSSPSLTILA 417 + G L+E S R G+ D G +A A AR++ + LA Sbjct: 301 CAEAVLGELVERFSALRCDAGEANADCGPLINARQKAGLEARLEAAQADGVRVAAQGALA 360 Query: 418 GGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPVLSVYVYPDDKYKETLQLVDSTTSYG 477 G + G+FV P ++ +++EE+FGPVL+V V+ D+ E L+L ++ T +G Sbjct: 361 AGAPEG--GHFVVPHLLTDIPAGHAVLREELFGPVLAVQVFRDE--TEALRLANA-TDFG 415 Query: 478 LTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTGSIVGQQPFGGARASGTNDKPG 533 L V+++D K +R +G +IN+ G + + PFGG SG + G Sbjct: 416 LCAGVWTRDGGRQLRLAKGIR--SGQVFINNYGAGGGI-ELPFGGVGRSGHGREKG 468 Lambda K H 0.319 0.135 0.411 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: 691 Number of extensions: 40 Number of successful extensions: 4 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: 563 Length of database: 486 Length adjustment: 35 Effective length of query: 528 Effective length of database: 451 Effective search space: 238128 Effective search space used: 238128 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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