Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate CA265_RS03610 CA265_RS03610 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >FitnessBrowser__Pedo557:CA265_RS03610 Length = 379 Score = 154 bits (388), Expect = 8e-42 Identities = 107/313 (34%), Positives = 155/313 (49%), Gaps = 63/313 (20%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L+KR+I CLDV+ D KG N ++R+ G PV+LA QY + GADE+ Sbjct: 130 LSKRIIPCLDVK-----DGRTVKG--------VNFVDLRDAGDPVELAAQYAQQGADELV 176 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT + MI++++ ++ + +P T+GGGI + DA Sbjct: 177 FLDITATHE---RRKTMIEMVKSVARQLNIPFTIGGGITEIADAEA-----------LLN 222 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADKISI S AV +E +++ +G Q VV+++D + V Sbjct: 223 AGADKISINSAAVR------------NPKLIEDLAKTFGVQFVVLAVDTKYV-------- 262 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 G N ++GGR + K E+LGAGEILL +D DG Sbjct: 263 ---------DGKN-------MVHLNGGRLITELETENWIKQAEDLGAGEILLTSMDHDGT 306 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 GFD L+ ++ + IP+IAS GAG HF+EVF+K N AALAA +FH E+ I + Sbjct: 307 KAGFDCGLLSKVNQMINIPIIASGGAGNMAHFTEVFQKANVDAALAASVFHYGEILIPDL 366 Query: 580 KEHLQEERIEVRI 592 K+ L+ I VRI Sbjct: 367 KQELKRNNIPVRI 379 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: 446 Number of extensions: 26 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: 379 Length adjustment: 33 Effective length of query: 559 Effective length of database: 346 Effective search space: 193414 Effective search space used: 193414 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: 51 (24.3 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