Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_043769573.1 U743_RS15680 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000733765.1:WP_043769573.1 Length = 261 Score = 135 bits (341), Expect = 2e-36 Identities = 98/314 (31%), Positives = 152/314 (48%), Gaps = 60/314 (19%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 LAKR+I CLD+ D+G +V KG ++ ++ + G PV++AG+Y GADE+ Sbjct: 2 LAKRIIPCLDI---DRGRVV--KGVKF--------RDIVDAGDPVEVAGRYDAQGADELV 48 Query: 340 FLNITGFRDFPLGDLP-MIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYF 398 FL+IT + D P + + Q ++ +++P TVGGG+R D Sbjct: 49 FLDITASHE----DRPTLFATVEQVARQIYIPFTVGGGVRTCADVRA-----------LL 93 Query: 399 RSGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDD 458 +GADK++I + AV + ++ + YG Q +VV++D +RV N + Sbjct: 94 SAGADKVAINTAAVIDPDFVTEAAGR------------YGVQCIVVAVDAKRV--NKRKE 139 Query: 459 VPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDG 518 P ++ GGR+ + A E + + E GAGE+LL +D DG Sbjct: 140 PPR-----------------WEVFTHGGRKATGLDAVEWCQTMVEKGAGELLLTSMDKDG 182 Query: 519 QGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQS 578 G+D +L++ IS V +P+IAS G G H E + A A LAA IFH+ + Sbjct: 183 TKSGYDTELLRAISSHVPVPLIASGGVGNLQHLYEGLAEGEADAVLAASIFHQGTHSVGE 242 Query: 579 VKEHLQEERIEVRI 592 K L E I VR+ Sbjct: 243 AKAFLAERGINVRL 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: 350 Number of extensions: 25 Number of successful extensions: 6 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: 261 Length adjustment: 31 Effective length of query: 561 Effective length of database: 230 Effective search space: 129030 Effective search space used: 129030 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 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