Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate 201225 SO2068 hisF protein (cyclase) (NCBI ptt file)
Query= BRENDA::Q9SZ30 (592 letters) >FitnessBrowser__MR1:201225 Length = 257 Score = 126 bits (316), Expect = 1e-33 Identities = 97/312 (31%), Positives = 148/312 (47%), Gaps = 57/312 (18%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 LAKR++ CLDV+ D V KG Q+ +E+ +G V LA +Y +GADE+ Sbjct: 2 LAKRIVPCLDVK-----DGCVVKGVQF------RNHEI--VGDIVPLAARYAAEGADELV 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 F +IT + D + + ++ + +P V GGI+ T A E Sbjct: 49 FYDITASAHDRVVDKSWVS---RVAEQIDIPFCVAGGIKTITQAR-----------ELLA 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 GADKIS+ S A+S S + ++ +G Q +V+ ID + + D Sbjct: 95 FGADKISVNSPALS------------DPSLISRLQDEFGRQCIVIGIDS---FYDAASD- 138 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 YKV + T +E AWY + + V++ G GEI+LN ++ DG Sbjct: 139 SYKVKQFTGDEAATKETAWY--------------TQDWVEEVQKRGCGEIVLNVMNQDGV 184 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 G+DI + L+ +P+IAS GAGT HF +VF AALAA +FH+ + I + Sbjct: 185 RGGYDIKQLSLVRQLCDVPLIASGGAGTMAHFRDVFIDAKVDAALAASVFHKAIINIGEL 244 Query: 580 KEHLQEERIEVR 591 K++L E I +R Sbjct: 245 KQYLAAEGIAIR 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: 326 Number of extensions: 19 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: 257 Length adjustment: 30 Effective length of query: 562 Effective length of database: 227 Effective search space: 127574 Effective search space used: 127574 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