Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_011840686.1 RSPH17029_RS04670 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000015985.1:WP_011840686.1 Length = 253 Score = 131 bits (329), Expect = 4e-35 Identities = 106/313 (33%), Positives = 143/313 (45%), Gaps = 62/313 (19%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L R+I CLDV D V KG N ++R+ G PV+ A Y GADE+ Sbjct: 2 LKTRIIPCLDV-----ADGRVVKG--------VNFVDLRDAGDPVEAARAYDAAGADELC 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+I + M ++ +T++ F+PLTVGGG+R D Sbjct: 49 FLDIHATHE---NRGTMYDLVTRTAEQCFMPLTVGGGVRTHQDVRA-----------LLL 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADK+S S AV+ + + + + +G+Q +VV+ID + V Sbjct: 95 AGADKVSFNSAAVA------------DPTVVAEAADRFGSQCIVVAIDAKTVA------- 135 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 PG ++ GGR I A A V GAGEILL +D DG Sbjct: 136 ---------PGR-------WEIFTHGGRRATGIDAVAFACDVASRGAGEILLTSMDRDGT 179 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 GF++ L + ISD+V IPVIAS G GT DH E + ASA LAA IFH E I Sbjct: 180 RAGFNLPLTRAISDAVPIPVIASGGVGTLDHLVEGVTEGGASAVLAASIFHFGEFTIGEA 239 Query: 580 KEHLQEERIEVRI 592 K H+ I VR+ Sbjct: 240 KAHMASAGIPVRL 252 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: 333 Number of extensions: 23 Number of successful extensions: 4 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 16 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