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 H281DRAFT_05659 H281DRAFT_05659 imidazole glycerol phosphate synthase subunit hisF
Query= curated2:Q3ZYM9 (244 letters) >FitnessBrowser__Burk376:H281DRAFT_05659 Length = 257 Score = 133 bits (334), Expect = 4e-36 Identities = 82/231 (35%), Positives = 129/231 (55%), Gaps = 13/231 (5%) Query: 10 IIPAIDILGGRCVRLFQGDYAQETVYSSDPVGTAMRWQSLGAPRLHVVDLDGAADGQSVN 69 IIP +D+ GR V+ G E + DPV A R+ GA L +D+ +D + + Sbjct: 7 IIPCLDVTAGRVVK---GVNFVELRDAGDPVEIARRYDDQGADELTFLDITATSDQRDLI 63 Query: 70 FELIKEIANSALIPVEVGGGIRSMETVKKLLVAGVDRVILGTAAVENPELVKEICARY-A 128 +I+ +A+ IP+ VGGG+R++E V++LL AG D++ + ++AV NP+LVK+ +Y + Sbjct: 64 LPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISMNSSAVANPQLVKDATDKYGS 123 Query: 129 DSVAVSIDAR---------NGKVATRGWVTNTEIDALELARSMKKLGIRRFIYTDISRDG 179 + V+IDA+ +V T G T ++A+E AR M +LG + T + RDG Sbjct: 124 QCIVVAIDAKRVSADGETPRWEVFTHGGRKATGLEAVEWARKMAELGAGEILLTSMDRDG 183 Query: 180 TLSEPNFAAIRDLISAINVPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIY 230 T S + A R + A+ VPVIASGGV +L HL G A++ +I+ Sbjct: 184 TKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLADGITSGHADAVLAASIF 234 Score = 26.2 bits (56), Expect = 7e-04 Identities = 16/98 (16%), Positives = 40/98 (40%) Query: 38 DPVGTAMRWQSLGAPRLHVVDLDGAADGQSVNFELIKEIANSALIPVEVGGGIRSMETVK 97 + V A + LGA + + +D + L + ++++ +PV GG+ +++ + Sbjct: 158 EAVEWARKMAELGAGEILLTSMDRDGTKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLA 217 Query: 98 KLLVAGVDRVILGTAAVENPELVKEICARYADSVAVSI 135 + +G +L + E R+ +S+ Sbjct: 218 DGITSGHADAVLAASIFHYGEHTVGEAKRFMAEQGISV 255 Lambda K H 0.319 0.137 0.386 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: 175 Number of extensions: 12 Number of successful extensions: 5 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: 244 Length of database: 257 Length adjustment: 24 Effective length of query: 220 Effective length of database: 233 Effective search space: 51260 Effective search space used: 51260 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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