Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate YP_002822676.1 NGR_b04600 aldehyde dehydrogenase
Query= BRENDA::P30038 (563 letters) >NCBI__GCF_000018545.1:YP_002822676.1 Length = 502 Score = 148 bits (374), Expect = 4e-40 Identities = 131/433 (30%), Positives = 205/433 (47%), Gaps = 35/433 (8%) Query: 108 AALAARKEWD------LKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQGKTVIQA-EI 160 A AAR+++D LKP+ +R ++ AD++ E+ + GK+V A EI Sbjct: 68 AVRAARRQFDGGAWRRLKPL-ERERLLHSLADLIEA-HSDELAEIEAIDMGKSVTFAREI 125 Query: 161 DAAAELIDFFRFNAKYAVELEGQQPISVPPST--NSTVYRGLE--GFVAAISPFNFT--A 214 D +D FR+ A +A +L G+ +V PS N Y E G VAAI P+NF Sbjct: 126 DIRGT-VDTFRYFAGWASKLHGR---TVEPSLPGNYLAYTRKEPLGVVAAIVPWNFPLQT 181 Query: 215 IGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDTVT 274 + LA A A+ G + KP++ L++ +++EAG+P ++ V G + G ++ Sbjct: 182 LAWKLAAALAV-GCTAIVKPAELTSLSTLRFAELVQEAGIPDGVVNIVTGKGSIIGAAMS 240 Query: 275 SSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESVVS 334 + + + FTGS P + + + NL + E GGK+ V AD++S Sbjct: 241 THPGINKVTFTGSTPVGQEVGRTAVGNL------KHVTLELGGKSPVLVLDDADLQSAAV 294 Query: 335 GTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDA 394 F GQ C A +R+YV S+ L+ S +K+ P D + ++ A Sbjct: 295 AVANGVFFNSGQVCDAGTRVYVQGSVHDAFLDELVSVTSALKIA-PGLDRDCYIGPLVSA 353 Query: 395 KSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPVLS 454 + + ++E R ++ GG G+F+EP I PQ I++EEIFGPVL Sbjct: 354 QQKKVVSGYIEAGRRE-GAELIHGGASLHRQGHFIEPAIFSHCKPQMSIVREEIFGPVL- 411 Query: 455 VYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTGSI 514 P D + + L + T +GL A++S D V T + R AG+ Y+N ST I Sbjct: 412 -VTSPFDDLDDAVSLAND-TPFGLAAAIYSNDLSRVH--TLIPRLHAGSIYVNAHST--I 465 Query: 515 VGQQPFGGARASG 527 PFGG +ASG Sbjct: 466 DPAMPFGGFKASG 478 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: 636 Number of extensions: 35 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: 502 Length adjustment: 35 Effective length of query: 528 Effective length of database: 467 Effective search space: 246576 Effective search space used: 246576 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