Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_092993135.1 BLP65_RS04695 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_900102855.1:WP_092993135.1 Length = 481 Score = 197 bits (500), Expect = 9e-55 Identities = 141/473 (29%), Positives = 232/473 (49%), Gaps = 26/473 (5%) Query: 50 DKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIR 109 + Q NPA +++ + + +AI++ A ++ + E R L A + Sbjct: 24 EPFQVTNPAN-GEVLAEIPAMGAEETRQAIEAGRHALES--SAGLETRRAWLQMIAEALT 80 Query: 110 RRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRP-GEQNRYF 168 + E L HE GKPWKE + A F Y A + I L + + +P G + Sbjct: 81 DNREEIGRILTHEHGKPWKEGIGEVDYAAGFFRY-AGENIGLLKPYTLQEQPRGLSWTVY 139 Query: 169 YTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDA-GLP 227 + P GV ++PWNF + ++ A + + V+KP+ TP+ ++L+ LP Sbjct: 140 HRPAGVVGLMTPWNFPIGMIAKKLSAALAADCSCVVKPSRKTPLTMIALFDLLDRTLDLP 199 Query: 228 KGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEM 287 G +N V G + D L++HP +I+FTGS VG +L ++A + +KR+ +E+ Sbjct: 200 PGKVNLVMGGACPITDTLMEHPHVRVISFTGSTAVGRQLIRKSA------DGIKRLTLEL 253 Query: 288 GGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNL 347 GG +V DADLD AAE ++ + F GQ C +R + + V E EK A L Sbjct: 254 GGNAPFIVFADADLDHAAEQLVSNKFRGGGQTCVCSNRIFVERPVAPEFAEKLAEKASAL 313 Query: 348 TVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTG----GEGDSSTGFFIQPTII 403 VG+ +R +GP+ID +EK+ S++ +G M GE ++ GFF +PT+I Sbjct: 314 RVGNGMDRVTDIGPLIDRSGYEKVRSHLTDALDKGAQMVSGGDPGEWSTARGFF-RPTVI 372 Query: 404 ADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRN--RAHIEQAKR 461 + P ++ +EE FGP+V ++ + + + AN+TE+GL + T + RA ++ Sbjct: 373 RGVAPGMLVTREETFGPLVPIAEFDSEEEVIARANDTEFGLAAYLFTADPERAGHVVSRL 432 Query: 462 EF-HVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513 EF HVG N PFGG K SG + GG + L ++ +TV++ Sbjct: 433 EFAHVG-----WNTGSGPTPEAPFGGMKQSGF-GREGGREGLVEFVETQTVAQ 479 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: 616 Number of extensions: 31 Number of successful extensions: 6 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: 481 Length adjustment: 34 Effective length of query: 481 Effective length of database: 447 Effective search space: 215007 Effective search space used: 215007 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