Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Synpcc7942_1829 Synpcc7942_1829 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= BRENDA::A4WHB6 (251 letters) >FitnessBrowser__SynE:Synpcc7942_1829 Length = 256 Score = 131 bits (330), Expect = 1e-35 Identities = 85/240 (35%), Positives = 129/240 (53%), Gaps = 9/240 (3%) Query: 5 VIPCLDMDGKAGVVVKGVNFEGVREVG-DPVEMAVRYEEEGADEIAILDITATPEGRSTF 63 VIP +D+ G V + +++ G DPV MA+R+ E GA + ++D+ EG Sbjct: 3 VIPAIDLLGGQCVRLFQGDYDQAEVYGKDPVGMALRWAEAGAQRLHLVDLDGAKEGSPVN 62 Query: 64 VESVRRVAEAVSIPVLVGGGVRGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFGS 123 E++ +A+ +SIPV VGGG+R + A L +G ++ + T AV+ P LV +A EF Sbjct: 63 AEAIATIAQRLSIPVQVGGGLRDRDTVARLLDSGVERAILGTVAVERPALVEALAGEFPG 122 Query: 124 QSTVVAIDAKLVGGRYEVFVRGGKEPTGLDAVEWAKKVEELGAGEILLTSIDKDGTRLGY 183 Q V IDA+ +V RG E +GL AV A+++ +LGA ++ T I +DGT G Sbjct: 123 Q-IAVGIDAR----SGKVATRGWLEDSGLTAVALAQQMADLGACALICTDIGRDGTLQGP 177 Query: 184 DVELIRRVAEAVKIPVIASGGAGALEHFYE---AAAAGADAVLAASLFHFRVLTISEVKR 240 ++E +R +A AV IPVIASGG G+L A G V+ + + + E R Sbjct: 178 NLEELRAIAAAVSIPVIASGGVGSLTDLLSLLPLEAQGVSGVIVGKALYTGAVDLQEALR 237 Lambda K H 0.318 0.136 0.375 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: 170 Number of extensions: 8 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: 251 Length of database: 256 Length adjustment: 24 Effective length of query: 227 Effective length of database: 232 Effective search space: 52664 Effective search space used: 52664 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: 47 (22.7 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