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 Ac3H11_4733 Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)
Query= curated2:Q3Z6V7 (237 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4733 Length = 250 Score = 122 bits (306), Expect = 7e-33 Identities = 70/213 (32%), Positives = 113/213 (53%), Gaps = 20/213 (9%) Query: 31 DPVGTAMRWQSLGAPRLHVVDLDGAADGESVNFELIREIANSALIPVEVGGGIRSMDTVK 90 DPV A R+ + GA L +D+ +DG + +I +A+ IP+ VGGG+R+++ V+ Sbjct: 15 DPVEIAARYNAQGADELTFLDITATSDGRDLILHIIEAVASQVFIPLTVGGGVRTVEDVR 74 Query: 91 KLLTAGVDRVILGTVAVENPELVREICARY-ADSVAVSIDAR------------NGKVAT 137 +LL AG D+ + A+ NP+L+ + A+Y A + V+IDA+ NG+ Sbjct: 75 RLLNAGADKTSFNSAAIANPDLINAVSAKYGAQCIVVAIDAKRRSAEDALRIGANGQPVG 134 Query: 138 RGW-------VNSTEVDALELARSMKKLGVKRFIYTDISRDGTLSEPNFAAIRDLISAIN 190 GW +T +DA+ A M + G + T + RDGT S + A R + A++ Sbjct: 135 EGWDVYSHGGRKNTGLDAIAWATEMARRGAGEILLTSMDRDGTKSGFDLALTRAVSDAVS 194 Query: 191 MPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIY 223 +PVIASGGV +L HL G A++ +I+ Sbjct: 195 VPVIASGGVGNLDHLADGVQQGGADAVLAASIF 227 Lambda K H 0.318 0.136 0.384 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: 181 Number of extensions: 16 Number of successful extensions: 4 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: 237 Length of database: 250 Length adjustment: 23 Effective length of query: 214 Effective length of database: 227 Effective search space: 48578 Effective search space used: 48578 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 (21.7 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