Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_040372522.1 B149_RS0108900 L-glutamate gamma-semialdehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000375485.1:WP_040372522.1 Length = 1008 Score = 476 bits (1225), Expect = e-138 Identities = 234/516 (45%), Positives = 334/516 (64%), Gaps = 4/516 (0%) Query: 2 LQPYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61 + P+ + P TDFT+ + R AF E + +E GK+YPL ING VTT+D + S+NPA+ Sbjct: 476 IPPFNNYPPTDFTIPSQRAAFPEEMKRWREETGKQYPLFINGREVTTDDTLDSYNPAKPS 535 Query: 62 QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121 +++G++ +A ++A+ A EA+ +WR+V+P++RA L+ AA R+ SA V Sbjct: 536 EIIGTICQAGTGEIDQAMDGAKEAYLSWRDVDPKKRAQYLLDAAEWCRKNVWRLSALQVL 595 Query: 122 EAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPW 181 E GK W +A AD EAIDF+EYYAR+MI L + + + PGE +RYFY GV I+PW Sbjct: 596 EVGKQWDQAQADVGEAIDFMEYYAREMIRLGDPRRMGNAPGEYSRYFYQGKGVAAVIAPW 655 Query: 182 NFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEV 241 NF AI VG A IV+G V+ KP+ + V+ + E+ + GLP GV NY PG G+ + Sbjct: 656 NFPFAISVGMVSAAIVSGCPVLYKPSGLSSVIGWQLAEMWREVGLPDGVFNYTPGRGSVI 715 Query: 242 GDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADL 301 GDY+V+HP +LI FTGS +VG+R+ E+AAV +PGQ KRVI EMGGK+ +++D DADL Sbjct: 716 GDYIVEHPDIALIAFTGSMEVGLRIQEKAAVKQPGQQQCKRVIAEMGGKNGIIIDDDADL 775 Query: 302 DLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGP 361 D A +L SAFGF GQKCSA SR ++ +YD + + A+++ +G NYMGP Sbjct: 776 DEAVLGVLYSAFGFQGQKCSACSRVIVLDSIYDRFVHRLREAAESVKLGPAEEPGNYMGP 835 Query: 362 VIDEKAFEKIMSYIEIGKKEGRLMTGGEGD----SSTGFFIQPTIIADLDPEAVIMQEEI 417 V+D+ A E +++Y +I +EG ++ E D + G ++ TI+ + PE I QEE+ Sbjct: 836 VVDKGAQENVLNYAKIAAEEGSVLVQREADEKYRADGGCYVPLTIVEGITPEHRIAQEEV 895 Query: 418 FGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGA 477 FGPV++ + DFD ALE AN+T++ LTGA+ +R+ ++E+ REF VGNLY N+ GA Sbjct: 896 FGPVLSVMRVKDFDQALEWANSTQFALTGAIYSRSPNNLERGAREFRVGNLYLNKPSVGA 955 Query: 478 IVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513 +V H FGGFKMSG SK+GGPDYL M + V E Sbjct: 956 LVERHAFGGFKMSGVGSKSGGPDYLLQFMDPRIVCE 991 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: 1201 Number of extensions: 62 Number of successful extensions: 2 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: 1008 Length adjustment: 40 Effective length of query: 475 Effective length of database: 968 Effective search space: 459800 Effective search space used: 459800 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: 55 (25.8 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