Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_013705296.1 DESAC_RS01435 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000195295.1:WP_013705296.1 Length = 259 Score = 155 bits (392), Expect = 2e-42 Identities = 106/313 (33%), Positives = 161/313 (51%), Gaps = 57/313 (18%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L+KR+I CLDVR TKG ++ + ++G PV +A YY+ GADEI Sbjct: 2 LSKRIIPCLDVRGGR-----TTKGIKF--------KDNVDIGDPVQMARFYYEQGADEIV 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 F +IT D MI V+R+ ++ +F+P +VGGGIR +LE E Sbjct: 49 FYDITASSD---RRNIMIDVVRRVAREIFIPFSVGGGIR-----------TLEDMREALL 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GA+K+S+ S AV I G +R +G+Q +V+ +D ++V Sbjct: 95 AGAEKVSVNSAAVQNPR-IIAEG-----------ARAFGSQCIVLGMDVKQVL------- 135 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 P+ + + Y+ ++GGR + A A+ LGAGEI LN ID DG Sbjct: 136 -----------PSADIPSGYEIVINGGRTRMSLDALWWAQEAVRLGAGEICLNSIDADGT 184 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 G++++L +LIS +V +PVIAS GAG P+H +V A AAL A I H + I + Sbjct: 185 QTGYELNLTRLISTAVSVPVIASGGAGMPEHLYDVLTIGQADAALIASIVHYGDYSIGDI 244 Query: 580 KEHLQEERIEVRI 592 K++LQ+ I++R+ Sbjct: 245 KDYLQQRGIKMRL 257 Lambda K H 0.317 0.135 0.391 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: 373 Number of extensions: 23 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: 592 Length of database: 259 Length adjustment: 30 Effective length of query: 562 Effective length of database: 229 Effective search space: 128698 Effective search space used: 128698 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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