Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate 5209750 Shew_2203 imidazole glycerol phosphate synthase subunit HisF (RefSeq)
Query= curated2:P62356 (235 letters) >FitnessBrowser__PV4:5209750 Length = 257 Score = 89.0 bits (219), Expect = 8e-23 Identities = 70/244 (28%), Positives = 114/244 (46%), Gaps = 22/244 (9%) Query: 2 RLIPAVDLKSGKAVRLYEGDPARETPYGDPVEAALRFQEEGATLLHLVDL-----DRALG 56 R++P +D++ GK V+ + GD V A R+ E A L D+ DR + Sbjct: 5 RIVPCLDVRDGKVVKGVQF--RNHEIVGDIVPLAARYAAESADELVFYDITASAHDRVV- 61 Query: 57 TGENREAVRRVAASLSIPFQLAGGIRSLEALQEALSLGASRAVVGTVAVKDPGLLARMLE 116 ++ V RVA + IPF +AGGI+S+E +E L+ GA + + + A+ DPGL+ R+ + Sbjct: 62 ---DKSWVSRVAEQIDIPFCVAGGIKSIEQAREKLAFGADKISINSPALSDPGLIDRLQD 118 Query: 117 AVGPDRLAVALDA------RGLEVVVSGWQEAASASALDLLRAWAE----MGVRTLLYTD 166 G + + +D+ +V EAA+ + W E G ++ Sbjct: 119 EFGRQCIVIGIDSYYDADTDSYKVKQFTGDEAATKDTQWYTQDWVEEVQRRGCGEIVLNV 178 Query: 167 VRRDGTLLGLDREVVARVRAAWPHELIVGGGIASPED-LHLLQALGVDGALIGKALYEGR 225 + +DG G D + +A VRA LI GG + E L + GVD AL ++G Sbjct: 179 MNQDGVRQGYDIKQLAMVRAICDVPLIASGGAGTMEHFLEVFTQAGVDAALAASVFHKGI 238 Query: 226 IRLK 229 I ++ Sbjct: 239 IEIE 242 Lambda K H 0.319 0.137 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: 127 Number of extensions: 10 Number of successful extensions: 5 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: 235 Length of database: 257 Length adjustment: 24 Effective length of query: 211 Effective length of database: 233 Effective search space: 49163 Effective search space used: 49163 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