Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_082353398.1 CDES_RS06155 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_001277995.1:WP_082353398.1 Length = 513 Score = 208 bits (529), Expect = 4e-58 Identities = 148/483 (30%), Positives = 233/483 (48%), Gaps = 14/483 (2%) Query: 38 PLIINGER-VTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEE 96 P IING V E + + +NPA + S+ A A+ +A WR Sbjct: 25 PHIINGHPLVEGERRGEVFNPAT-GAVTASLPFATTATVNAAVSAAQAVAPAWRATGLAR 83 Query: 97 RANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKE 156 RA ++ K II RK E +A + E GK +A + A ++ +E+ A + + Sbjct: 84 RAAVMFKLHEIITSRKDELAALITEEQGKVLSDAAGEIARGLENVEFCAGLVHHMKGEFL 143 Query: 157 ILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAK 216 + G P+GV I+P+NF + + I GNTVVLKP+ P Sbjct: 144 EQAAAGLDVHQVRQPLGVVACITPFNFPAMVPLWMITTAIAAGNTVVLKPSEKDPSAVNW 203 Query: 217 FVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPG 276 VE +AGLP+GV+N + G E + L+D P+ ++F GS + +Y RA + Sbjct: 204 IVEAFHEAGLPEGVLNLIHGD-REAVEALIDDPRVQAVSFVGSTPIAQSIYTRATALG-- 260 Query: 277 QNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEV 336 KRV G K+ +VV DADLD AA++ + + +G +G++C A S V D+ D++ Sbjct: 261 ----KRVQALGGAKNHMVVMPDADLDAAADAAVSAGYGAAGERCMAISVVVPVGDIADDL 316 Query: 337 LEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGR--LMTGGEGD-SS 393 + K + +LT+G+ T+ D+ MGPVI A E+I I G ++ G D Sbjct: 317 IAKISSRITDLTIGEGTDPDSEMGPVITSAAKERIEGLIAGSSDSGAEVVVDGRSVDLPD 376 Query: 394 TGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNR 453 GFFI PT+I + P + EEIFGPV++ ++ FD A+E+ N+ +Y A+ TR+ Sbjct: 377 EGFFIGPTLIDHVKPGMPVYDEEIFGPVLSVARVGHFDEAVELINSCQYANGTAIFTRDG 436 Query: 454 AHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMS-GTDSKAGGPDYLALHMQAKTVS 512 + + VG + N +G FGG+K S D+ GP+ + + K V+ Sbjct: 437 RTAREFEFAIEVGMVGINVPIP-VPIGAFSFGGWKKSLFGDTHMYGPESFNFYTRRKVVT 495 Query: 513 EMY 515 + Sbjct: 496 SRW 498 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: 618 Number of extensions: 30 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: 515 Length of database: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 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: 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