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 WP_011883057.1 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= curated2:A6TKT6 (252 letters) >NCBI__GCF_000016205.1:WP_011883057.1 Length = 251 Score = 112 bits (280), Expect = 7e-30 Identities = 69/211 (32%), Positives = 118/211 (55%), Gaps = 13/211 (6%) Query: 6 IIPCLDVRKGRVVKGVNFVDIKDAG----DPVALARAYNDQGADEIVFLDITASHEERYI 61 +IP +D++ G+ V+ + D+ A DP A+AR + D GA + +D+ + + Sbjct: 3 LIPAIDLKDGQCVR-LKQGDMDQATIFSEDPAAMARKWVDLGARRLHLVDLNGAFAGKPK 61 Query: 62 LLDVVKKTSEEIF--IPLTVGGGIRTVEDMRQIIKSGADKVSINSSAVKNPSMITDCARQ 119 L+ ++ EE+ IP+ +GGGIR++E + + + +G V I ++AVKNP + D Sbjct: 62 NLEAIEAILEEVGDEIPVQLGGGIRSLETIEKYLDAGLSYVIIGTAAVKNPGFLQDACTA 121 Query: 120 FGSQAVVIAMDVKRGADGRYEVYVRGGREKTGLEAVDWARRVAQLGAGEILLTSMDRDGT 179 F S ++++ +D K G +V G + TG E +D AR+ G I+ T + RDG Sbjct: 122 F-SGSIIVGLDAKDG-----KVATDGWSKLTGHEVIDLARKFEDYGVESIVYTDIGRDGM 175 Query: 180 KSGYDLEITKRISQAVNIPVIASGGAGSVQD 210 G +++ T +++QAV IPVIASGG ++ D Sbjct: 176 LQGINIDATVKLAQAVGIPVIASGGLSNLTD 206 Score = 37.7 bits (86), Expect = 2e-07 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 9/87 (10%) Query: 15 GRVVKGVNFVDIKDAGDP---------VALARAYNDQGADEIVFLDITASHEERYILLDV 65 G ++ G++ D K A D + LAR + D G + IV+ DI + I +D Sbjct: 124 GSIIVGLDAKDGKVATDGWSKLTGHEVIDLARKFEDYGVESIVYTDIGRDGMLQGINIDA 183 Query: 66 VKKTSEEIFIPLTVGGGIRTVEDMRQI 92 K ++ + IP+ GG+ + D+ + Sbjct: 184 TVKLAQAVGIPVIASGGLSNLTDIENL 210 Lambda K H 0.319 0.136 0.378 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: 179 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 252 Length of database: 251 Length adjustment: 24 Effective length of query: 228 Effective length of database: 227 Effective search space: 51756 Effective search space used: 51756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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