Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_028489491.1 Q394_RS0111975 2-hydroxymuconic semialdehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_000621325.1:WP_028489491.1 Length = 486 Score = 211 bits (537), Expect = 5e-59 Identities = 152/479 (31%), Positives = 223/479 (46%), Gaps = 40/479 (8%) Query: 55 SINPANKEEVVGTVSKATQDHAEKAIQAAAKAFE-TWRYTDPEERAAVLFRAVAKVRRKK 113 +INPA +++ G V +A + ++A+ AA A + W ER A+L + + + Sbjct: 23 NINPATNQQL-GIVHEAGKAEVDQAVAAANAALKGPWGKMPVAERMAILHKVADGINARF 81 Query: 114 HEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMI--ELAKGKPVNS-------REGE 164 EF + GKP A ID A + +L K P S +G Sbjct: 82 DEFLEAECLDTGKP-----KSLASHIDIPRGAANFKVFADLFKNVPTESFMLDTPDGKGA 136 Query: 165 RNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEE 224 N + P GV VI PWN +M + GNTVV+KP+ P EV+ Sbjct: 137 LNYAIRKPKGVIAVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPRTTTLLGEVMNA 196 Query: 225 SGLPKGVVNFVPGSGAE-VGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQ 283 +G+PKGV N + G G G++L HP + ITFTG G AA V+ H++ Sbjct: 197 AGVPKGVYNVIHGFGPNSAGEFLTTHPDINGITFTGETRTG------AAIVKASADHIRH 250 Query: 284 VIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIE 343 V E+GGK+ VV DCD++ A + S F GQ C R V +++E L R+ E Sbjct: 251 VSFELGGKNPAVVFADCDMDKAIEGTLRSVFANCGQVCLGTERVYVERPIFNEFLSRLTE 310 Query: 344 ITESKKVGEPDSADVYMGPVIDQASFNKIMDYIEIGKEEG-RLVSGG-----KGDDSKGY 397 E ++G D A MGP+I + K++ Y EEG L++GG G ++G Sbjct: 311 AAEGMQLGAWDDACTSMGPLISKEHQQKVLSYYAKAIEEGANLITGGGVPEMPGALAEGN 370 Query: 398 FIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHI 457 +++PTI+ L A +++EEIFGP S DE + AN+T+YGL AV T+N Sbjct: 371 WVQPTIWTGLPETATVVKEEIFGPCCHVQPFDSEDEVVAWANDTKYGLAAAVWTENTSRA 430 Query: 458 NRAKQEFHVG----NLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 512 +R + G N +F R+ PFGG K SG + GG L + + K + Sbjct: 431 HRVAAQLDAGIVWVNSWFLRDLR------TPFGGMKHSGI-GREGGVHSLEFYTELKNV 482 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: 579 Number of extensions: 31 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: 486 Length adjustment: 34 Effective length of query: 482 Effective length of database: 452 Effective search space: 217864 Effective search space used: 217864 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