Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_012101687.1 CKL_RS06400 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000016505.1:WP_012101687.1 Length = 253 Score = 172 bits (436), Expect = 1e-47 Identities = 117/313 (37%), Positives = 161/313 (51%), Gaps = 61/313 (19%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L KR++ CLDV V KG N ++++G PVD+A Y K GADEI Sbjct: 2 LTKRIVPCLDVNMGK-----VVKG--------INFVNLKDVGDPVDIAQYYNKQGADEIV 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT + +I V+ +T + VF+PLTVGGGI S ++ R Sbjct: 49 FLDITATYE---KRKTLIDVVERTGEKVFIPLTVGGGI-----------SGIDDFKIILR 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADKIS+ S A+ ++ K +G+Q VVV+ID ++ Sbjct: 95 AGADKISVNSAAIRNPNLIYEAADK------------FGSQCVVVAIDAKK--------- 133 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 E+ W + GGR+ I A E K VE LGAGEILL +D DG Sbjct: 134 ------------RAEDQGW-DVFIEGGRKNTGIDAIEWVKKVESLGAGEILLTSMDADGT 180 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 G+DI+L K +++SV IPVIAS G G+ + F +VFE T A AALAA +FH E+ I+ V Sbjct: 181 KNGYDIELTKAVAESVNIPVIASGGCGSLEDFYDVFEDTGADAALAASLFHYGELEIKDV 240 Query: 580 KEHLQEERIEVRI 592 KE+L + I VR+ Sbjct: 241 KEYLHKRDIPVRL 253 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: 379 Number of extensions: 23 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: 253 Length adjustment: 30 Effective length of query: 562 Effective length of database: 223 Effective search space: 125326 Effective search space used: 125326 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