Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011032788.1 MM_RS04385 aldehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_000007065.1:WP_011032788.1 Length = 479 Score = 261 bits (668), Expect = 3e-74 Identities = 163/462 (35%), Positives = 244/462 (52%), Gaps = 17/462 (3%) Query: 57 NPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHEF 116 NPA E ++ V + T++ A++AA AFE W P++R V +RA VR++K E Sbjct: 25 NPATCE-LLEQVPRGTEEDVALAVEAALSAFEGWASISPQQRGMVFYRAAGLVRQRKEEL 83 Query: 117 SALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTGVT 176 +ALL +E GKP EA + +EYY L +G + + V P GV Sbjct: 84 AALLTQEQGKPLAEARNELEGFSHVLEYYCGLAGSL-RGDFIPVTGNGYSFTVKKPLGVC 142 Query: 177 VVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVP 236 I PWN IM +++GNT VLKPAS+ P+ +L E+GLP GV+N V Sbjct: 143 AAIIPWNMPALIMGWKIAPALISGNTFVLKPASSTPLTNLTLASILNEAGLPAGVLNVVT 202 Query: 237 GSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVV 296 GSG G+ LV P I+FTG G RI E AA + +K+V E+GG D ++V Sbjct: 203 GSGEIAGESLVRSPDVRKISFTGESGTGKRISELAA------SGMKRVTLELGGSDPMIV 256 Query: 297 DEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPDSA 356 +D ++E A F GQ C+A R V E V E ++++ E + KVG Sbjct: 257 CDDANLESAVAGAIRGRFYNCGQTCTAVKRLYVFESVAREFIRKLEEGVKRLKVGNGLDK 316 Query: 357 DVYMGPVIDQASFNKIMDYIE--IGKEEGRLVSGGKGDD----SKGYFIEPTIFADLDPK 410 D MGP+ + + F I + + K EGR+++GGK KGYF EPT+ +D+ Sbjct: 317 DTDMGPLNNHSQFEYIKELVAGIEEKGEGRIIAGGKAPSFKGMGKGYFFEPTLVSDVPGD 376 Query: 411 ARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLY 470 +RL++EE+FGP++ V + DEA+E AN + YGL ++ TK+ D I ++ + G ++ Sbjct: 377 SRLLKEEVFGPLLPIVTVRNLDEAIEEANRSIYGLGASIWTKDLDRIRMGCEQLNAGIIW 436 Query: 471 FNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 512 N++ + PFGG K SG + GPD L+ +++ +TI Sbjct: 437 VNQHL--KVAPEVPFGGVKESGF-GRENGPDILSEYLETRTI 475 Lambda K H 0.315 0.133 0.382 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: 544 Number of extensions: 28 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: 516 Length of database: 479 Length adjustment: 34 Effective length of query: 482 Effective length of database: 445 Effective search space: 214490 Effective search space used: 214490 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