Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_028315369.1 G491_RS0116435 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000429905.1:WP_028315369.1 Length = 1204 Score = 238 bits (608), Expect = 7e-67 Identities = 164/523 (31%), Positives = 262/523 (50%), Gaps = 36/523 (6%) Query: 5 YKHEPFTDFTVEAN---RKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61 + +E TD+++ AN K+ + + E + P+++ GE + D ++ + AR D Sbjct: 488 FTNEADTDWSLLANVDWAKSIRDKWMMDEGAEPAQVPIVVAGEEIFDRDPREAIDSARYD 547 Query: 62 Q------LVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115 + +V + + A + A+KA+++A WR+ + +ER IL K A +R+ + + Sbjct: 548 EKTGQRIVVANYAMATAEDADKAVETAKADPDGWRSKSLDERHAILDKVAHELRKARGDL 607 Query: 116 SAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVT 175 GK + EAD + +EA+DF+E+Y I + TP GV Sbjct: 608 IGAAAANTGKVFTEADPEVSEAVDFVEFYPHSAKLFENLPNIKA----------TPKGVG 657 Query: 176 VTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVP 235 + ++PWNF +AI G + + GNTV+ KPAS V A + V+ AG+ K + ++P Sbjct: 658 LVVTPWNFPIAIPCGGMASALAAGNTVIFKPASAAVVTAWELVQCFYRAGVSKNALQFLP 717 Query: 236 GSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVV 295 SG EVG LV++P + TG D G+ + ++ RP + E GGK+ +V Sbjct: 718 CSGGEVGPRLVNNPDVDFVILTGGTDTGMEMLKQ----RPDM----FLAAETGGKNATIV 769 Query: 296 DRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVY-DEVLEKTVA-LAKNLTVGDPT 353 +D D A ++IL SAF GQKCSA S ++ K+VY DE+ K +A AK+ VG Sbjct: 770 TAMSDRDQAIKNILHSAFSNCGQKCSATSLVILEKEVYEDELFRKQLADAAKSFKVGSCW 829 Query: 354 NRDNYMGPVI--DEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAV 411 N MGP+I + +K ++ +E G+ + E + + P I + P + Sbjct: 830 KFRNKMGPLIHPPKGDLKKALTTLEPGES---WVLQPEQVGNNPYLWTPGIKWGVKPGSY 886 Query: 412 IMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFN 471 E FGP++ +A D +HA+E+ N T YGLT + + + + K GNLY N Sbjct: 887 THMTEFFGPLIGVMEAKDLNHAMELVNQTGYGLTSGLESLDHREQLKWKDGIKAGNLYIN 946 Query: 472 RNCTGAIVGYHPFGGFKMS--GTDSKAGGPDYLALHMQAKTVS 512 + TGAIV PFGG + S G KAG P+Y+ M + VS Sbjct: 947 KGTTGAIVLRQPFGGMRKSALGAGIKAGSPNYVYQFMDFEDVS 989 Lambda K H 0.316 0.134 0.388 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: 1409 Number of extensions: 70 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: 515 Length of database: 1204 Length adjustment: 41 Effective length of query: 474 Effective length of database: 1163 Effective search space: 551262 Effective search space used: 551262 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 (21.6 bits) S2: 55 (25.8 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