Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_017600194.1 D471_RS0119655 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000341125.1:WP_017600194.1 Length = 257 Score = 154 bits (390), Expect = 3e-42 Identities = 113/313 (36%), Positives = 156/313 (49%), Gaps = 59/313 (18%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 LA RVI CLDV D G +V KG ++ +R+ G PV+LAG Y GADE++ Sbjct: 3 LAIRVIPCLDV---DAGRVV--KGVNFE--------NLRDAGDPVELAGTYDAGGADELT 49 Query: 340 FLNITGFRDFPLGDLPMI-QVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYF 398 FL++T GD V+R+T+ VF+PLTVGGG+R D Sbjct: 50 FLDVTASS----GDRETTYDVVRRTADQVFIPLTVGGGVRTTDDVD-----------TLL 94 Query: 399 RSGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDD 458 R+GADK+ + + A++ E + +I+ +G Q +V+S D RRV Sbjct: 95 RAGADKVGVNTAAIARPE------------LIGEIAERFGRQVLVLSADVRRVRDGD--- 139 Query: 459 VPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDG 518 P P+G ++ T GGR G I A E + LGAGEILLN +D DG Sbjct: 140 ---------EPTPSG-----FEVTTHGGRRGTGIDALEWCERAAALGAGEILLNSMDADG 185 Query: 519 QGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQS 578 +GFD++L++ + V +P+IAS GAG +HF A A LAA +FH E I Sbjct: 186 TKEGFDLELIRAVRARVDVPLIASGGAGAVEHFVPAV-AAGADAVLAATVFHFGEFTIAD 244 Query: 579 VKEHLQEERIEVR 591 VK L+E VR Sbjct: 245 VKASLREAGYAVR 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: 390 Number of extensions: 33 Number of successful extensions: 7 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: 257 Length adjustment: 30 Effective length of query: 562 Effective length of database: 227 Effective search space: 127574 Effective search space used: 127574 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 10 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