Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_066921410.1 ACG33_RS11730 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_001579945.1:WP_066921410.1 Length = 476 Score = 229 bits (585), Expect = 1e-64 Identities = 147/477 (30%), Positives = 236/477 (49%), Gaps = 15/477 (3%) Query: 33 LGKEYPLIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNV 92 + K I GE VT++ + +PA Q++G V + + ++AI A A W N+ Sbjct: 3 ISKREACFIGGEWVTSDQWMDVDDPAT-GQVIGRVPRLGRRETQQAIAIAARAMGAWANL 61 Query: 93 NPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELN 152 +ERA L + +I + +A L E GKP EA A+ A F+E+++ + + Sbjct: 62 TGKERARTLRRYYELIIDNQESLAALLTQEQGKPLTEALAEIIYAASFIEWFSEEAKRVY 121 Query: 153 RGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPV 212 P ++ P+GV I+PWNF A++ + G +V++KPA+ TP Sbjct: 122 GDVIPGHAPDKRIIVLKQPIGVVAAITPWNFPAAMITRKIGPALAAGCSVIVKPAAQTPF 181 Query: 213 VAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAV 272 A E+ AGLP GV+N + G AE+G L ++FTGS +VG +LY + A Sbjct: 182 TALALAELGAQAGLPNGVLNVLTGGAAEIGGALTASETVRKLSFTGSTEVGAKLYAQCAP 241 Query: 273 VRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDV 332 +K++ +E+GG +V DADLD A + S F +GQ C +R H+ + Sbjct: 242 T------IKKLSLELGGNAPFIVCDDADLDAAVTGAIQSKFRNAGQTCVCANRIYAHEKI 295 Query: 333 YDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGD 391 +D +EK L V +++GP+IDE+A +K+ +IE ++G R++TGG Sbjct: 296 HDAFIEKLAVAVSALHVAPGCEPGSHIGPLIDERAVQKVREHIEDAVQKGARIVTGGAPH 355 Query: 392 SSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITR 451 + G F PT+IA+++ + ++ +EE FGP+ + D A+ AN T +GL R Sbjct: 356 ARGGRFFTPTVIAEVNQDMIVSREETFGPLAPVFRFRDDAEAITQANATPFGLAAYFYAR 415 Query: 452 NRAHIEQAKREFHVGNLYFNRNCTGAI-VGYHPFGGFKMSG---TDSKAGGPDYLAL 504 + + + + G + N TG I PFGG K SG SK G D+L + Sbjct: 416 DLGRVWRIAEQLEAGIIGVN---TGLISTELAPFGGVKASGLGREGSKYGMDDFLEI 469 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: 25 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: 476 Length adjustment: 34 Effective length of query: 481 Effective length of database: 442 Effective search space: 212602 Effective search space used: 212602 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