Align Imidazole glycerol phosphate synthase subunit HisF; EC 4.3.2.10; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF (uncharacterized)
to candidate GFF911 PGA1_c09270 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase HisA
Query= curated2:A4YI34 (251 letters) >FitnessBrowser__Phaeo:GFF911 Length = 240 Score = 109 bits (272), Expect = 6e-29 Identities = 77/239 (32%), Positives = 114/239 (47%), Gaps = 11/239 (4%) Query: 10 LDVKDGKVVK---GVRFLDLKLKGDPAELASRYEEEGADEIVFLDISATVEGRKTLLEKV 66 +D+KDG+ V+ G DPA A + E G D + +D++ G V Sbjct: 7 IDLKDGQAVRLLHGDMEKTTVFNDDPAAQALEFVEAGCDWLHLVDLNGAFAGEPVNAAPV 66 Query: 67 RETASVLSIPLTVGGGVRTVEDVSNLLSNGADKVSLNTVAAENPSVVSMASREFGAQAVV 126 + +P +GGG+R + + + G +V L TVA ENP +V A+R F + V Sbjct: 67 EKILKRCKVPAQLGGGIRDMATIERWIDKGLARVILGTVAVENPDLVREAARAFPGK-VA 125 Query: 127 VAIDAKRVGNGWRVFVRSGTKDTGLDAVDWAKRVEEMGAGEILLTSIDRDGTRDGYDLEL 186 V IDA+ NG RV + ++T + D AK E+ G I+ T I RDG G ++E Sbjct: 126 VGIDAR---NG-RVATKGWAEETDVMVTDLAKSFEDAGVAAIIYTDILRDGAMKGPNVEA 181 Query: 187 TKAVVRATKVPVIASGGAGKPDHFLSVFRQAGA--DAALAAGIFHDGVIRIRELKDYLK 243 T A+ A +PVIASGG L + GA + A++ +DG I + E LK Sbjct: 182 TAALANAVSIPVIASGGVSSLAD-LQALKSCGAPLNGAISGRALYDGAIDLGEALKILK 239 Lambda K H 0.317 0.135 0.374 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: 147 Number of extensions: 12 Number of successful extensions: 3 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: 251 Length of database: 240 Length adjustment: 24 Effective length of query: 227 Effective length of database: 216 Effective search space: 49032 Effective search space used: 49032 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: 46 (22.3 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