Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate GFF1767 PGA1_c17910 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase-like protein
Query= reanno::Caulo:CCNA_03852 (244 letters) >FitnessBrowser__Phaeo:GFF1767 Length = 247 Score = 185 bits (469), Expect = 8e-52 Identities = 101/240 (42%), Positives = 143/240 (59%), Gaps = 3/240 (1%) Query: 4 MILYPAIDLKDGQCVRLLHGDMDKATVFNTSPADQAQRFVQDGFSWLHVVDLNGAIEGKS 63 M++YP ++LKDG+CV L G +D A V++ P A F DG W+H+ D + AIEG + Sbjct: 1 MMIYPTMELKDGRCVTLDKGRLDTAMVWHVDPVATACSFAADGAEWMHLTDFD-AIEGDN 59 Query: 64 VNTAAVEQILESISIPVQLGGGIRTLEGVEAWIEAGVSRVILGTVAVHDPELVKKAARLW 123 N VE+I+ + IPVQLGGG+R+ E VE WI+ G RV++GT+A DPE+V+ RL+ Sbjct: 60 RNAGLVEEIIRTAGIPVQLGGGMRSREHVEHWIDKGAGRVVVGTLAAQDPEMVRMLTRLY 119 Query: 124 PEQIAVAVDVRDGKVAVDGWTGLSDLSAIDLSRRFEDAGVAALIITDISRDGALTGVNVE 183 P+QI +AVDV +G+V DGW + F D A +IITDI D + + Sbjct: 120 PDQIVLAVDVWEGQVMTDGWRQAGSFTPEAFIEAFADCPFAGIIITDIESDMSDVEAQLG 179 Query: 184 GVGELADAVSIPVIASGGVAAVADIERLKARQGVEIAGAILGRSLYAGTIKPSEALIAAA 243 + LA+ PVIASG V D+ RLK V +G ++GR+L+ T+ +EAL AA Sbjct: 180 LIAGLAEKARTPVIASGVVRTADDVARLKYIGSV--SGTLVGRALFRKTLTLAEALEEAA 237 Lambda K H 0.318 0.135 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: 197 Number of extensions: 12 Number of successful extensions: 3 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: 244 Length of database: 247 Length adjustment: 24 Effective length of query: 220 Effective length of database: 223 Effective search space: 49060 Effective search space used: 49060 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