Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate Echvi_0870 Echvi_0870 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase
Query= reanno::Btheta:350907 (239 letters) >FitnessBrowser__Cola:Echvi_0870 Length = 248 Score = 233 bits (593), Expect = 3e-66 Identities = 112/241 (46%), Positives = 168/241 (69%), Gaps = 2/241 (0%) Query: 1 MIEIIPAIDIIDGKCVRLSQGDYDSKKVYNENPVEVAKEFEANGVRRLHVVDLDGAASHH 60 M EIIP+I II+GKCVRL +GD+ +++V ++NP+E+A+EFE G+ R+H+VDLDGA Sbjct: 1 MFEIIPSIWIINGKCVRLKKGDFTTEQVISDNPLEIAQEFENCGIERIHLVDLDGARRGS 60 Query: 61 VVNHRVLEQIATRTSLIVDFGGGVKSDEDLKIAFESGAQMVTGGSVAVKDPELFCHWLEV 120 N+ +L I+ TSLIVDF GGV +D D+ FE GA+ +T +VA PE F WL Sbjct: 61 PKNYHILHTISAYTSLIVDFTGGVGTDGDIIKVFEHGAKTITAATVAANSPEKFSQWLIS 120 Query: 121 YGSEKIILGADV--KEHKIAVNGWKDESACELFPFLEDYINKGIQKVICTDISCDGMLKG 178 YG EKI + AD K+H I + GW+ + L+ + + ++G++ + C+DI+ +G+++G Sbjct: 121 YGREKINMAADTDPKDHLIKIKGWQKNTDIHLYDQISYFYDRGLKYLKCSDITREGVMEG 180 Query: 179 PSIDLYKEMLEKFPNLYLMASGGVSNVDDIIALNEAGVPGVIFGKALYEGHITLKDLRIF 238 P+ LY+E++ +FPNL+L+ASGGV NVDD L E G+ GV+FGKA Y G+IT ++L+ F Sbjct: 181 PNFKLYEEIIARFPNLHLVASGGVRNVDDFKRLKELGLRGVVFGKAYYSGNITAEELKTF 240 Query: 239 L 239 + Sbjct: 241 V 241 Lambda K H 0.320 0.140 0.413 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: 174 Number of extensions: 10 Number of successful extensions: 2 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: 239 Length of database: 248 Length adjustment: 23 Effective length of query: 216 Effective length of database: 225 Effective search space: 48600 Effective search space used: 48600 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 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