Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_011842504.1 RSPH17029_RS18285 dihydroxy-acid dehydratase family protein
Query= reanno::WCS417:GFF2156 (578 letters) >NCBI__GCF_000015985.1:WP_011842504.1 Length = 599 Score = 443 bits (1140), Expect = e-129 Identities = 256/552 (46%), Positives = 330/552 (59%), Gaps = 23/552 (4%) Query: 8 LRSAQWFGTADKNGF--MYRSWMKNQGIADHQFHG-KPIIGICNTWSELTPCNAHFRQIA 64 LRS WF D +Y N G+ + G KPIIGI T S+L+PCN H ++A Sbjct: 12 LRSRLWFNNPDDPEMTALYLERYLNYGLTRAELQGGKPIIGIAQTGSDLSPCNRHHIELA 71 Query: 65 EHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGC 124 + V+ G+ AGG P+E PV E+ RPTA L RNLA + + EA+ G PIDGVVL GC Sbjct: 72 KRVRDGITAAGGIPMEIPVHPIQETGKRPTASLDRNLAYLGLVEALHGYPIDGVVLTIGC 131 Query: 125 DKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFL 184 DKTTPALLM AA+ ++PAI + GPMLNG H+G+ GSGT VW+ E + G I + F Sbjct: 132 DKTTPALLMAAATVNIPAIAYSVGPMLNGWHRGERAGSGTAVWRARELLARGEIDEEGFY 191 Query: 185 AAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEM 244 + S G CNTMGTASTM +AE LG LP +AAIPA R + H +G R VEM Sbjct: 192 ELVASSAPSVGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAPYRERGQMGHATGRRIVEM 251 Query: 245 VREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMP 304 V EDL+ S ILT+EAFENAI +A+GGSTNA IHL A+A GV LD DDW R+G +P Sbjct: 252 VWEDLRPSDILTREAFENAIVACSALGGSTNAPIHLNAVARHAGVALDNDDWQRLGHAVP 311 Query: 305 TIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDSPIYGQ 364 +V+LQP+G +L E+FY AGG+PAVL L A+L+PHP A TV G L S + Sbjct: 312 LLVNLQPAGTYLGEDFYRAGGVPAVLGELLAADLLPHPEAPTVFGTPLSAGAMRSL---E 368 Query: 365 DEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAASPALMQH-----------RGRAVV 413 +VIR + P++ + G L GNL A++K S SP G V Sbjct: 369 TDVIRPVVEPLKGEAGFINLSGNLFD-SAIMKTSVISPDFRARYLSDPADPEAFEGTVFV 427 Query: 414 FENFDMYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRI 473 F+ + + A I+DP L + +++LVM+ GP GYPG AEV NM PA LL +G+ + I Sbjct: 428 FDGPEHFHAVIDDPALGMGEDAVLVMRGAGPLGYPGAAEVVNMRPPAYLLKRGIPAVPCI 487 Query: 474 SDARMSGTAYGTVVLHVAPEAAAGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMAD 533 D R SGT+ +L+ +PEAAAGG LA ++ GD I +D GR+ + +PD EL AR Sbjct: 488 GDGRQSGTSGSPSILNASPEAAAGGGLALLRNGDRIRVDLRRGRVDVLLPDEELEARRTA 547 Query: 534 LAPPQKLIVGGY 545 LA GGY Sbjct: 548 LAE-----AGGY 554 Lambda K H 0.319 0.136 0.413 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: 1045 Number of extensions: 66 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: 578 Length of database: 599 Length adjustment: 37 Effective length of query: 541 Effective length of database: 562 Effective search space: 304042 Effective search space used: 304042 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 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