Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_012173017.1 AZC_RS23060 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000010525.1:WP_012173017.1 Length = 258 Score = 150 bits (379), Expect = 6e-41 Identities = 108/313 (34%), Positives = 158/313 (50%), Gaps = 58/313 (18%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L RVI CLDV+ D V KG Q+ ++R+ G PV+ A Y GADE++ Sbjct: 2 LKVRVIPCLDVK-----DGRVVKGVQFV--------DLRDAGDPVESARAYDAAGADELT 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT + ++ V+R+T++ F+PLTVGGG+R D + Sbjct: 49 FLDITASHE---NRGTILDVVRRTAEQCFMPLTVGGGVRTVEDVRA-----------LLQ 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADK+SI + AV ++ + + + +G Q +VV+ID ++V Sbjct: 95 AGADKVSINTAAVHR------------RAFVGEAAEKFGEQCIVVAIDAKQV-------- 134 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 GP GE W + GGR+ + E A+ V +LGAGEILL +D DG Sbjct: 135 ---------SGP-GETPRW-EIFTHGGRKPTGLDVVEYAREVVDLGAGEILLTSMDRDGT 183 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 GKGFD L + ++D+V +PVIAS G GT DH + + A+A LAA IFH ++ Sbjct: 184 GKGFDTALTRAVADAVQVPVIASGGVGTLDHMVDGIREGGATAVLAASIFHFGTFTVRQA 243 Query: 580 KEHLQEERIEVRI 592 KE L + VR+ Sbjct: 244 KERLAAAGLPVRM 256 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: 382 Number of extensions: 29 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: 592 Length of database: 258 Length adjustment: 30 Effective length of query: 562 Effective length of database: 228 Effective search space: 128136 Effective search space used: 128136 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 Jul 25 2024. The underlying query database was built on Jul 25 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