Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_050463927.1 AKL27_RS16435 phosphogluconate dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >NCBI__GCF_001189915.1:WP_050463927.1 Length = 616 Score = 191 bits (486), Expect = 6e-53 Identities = 152/513 (29%), Positives = 247/513 (48%), Gaps = 42/513 (8%) Query: 47 IGICNTWSELTPCNAHFRELAEYVKKGVHE-------AGGLPLEFPVMSLGETNLRPTAM 99 I I ++++++ + F + +K+ + AGG+P ++ G+T + ++ Sbjct: 70 IAIVSSYNDMLSAHQPFERFPQILKEAIRAEGGVAQFAGGVPAMCDGITQGQTGME-LSL 128 Query: 100 LFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAASC-NLPALAVSGGPMLNGRF 158 R+ +M ++ N D V+ L CDK P LL+GA +LPA+ V GPM +G Sbjct: 129 FSRDTIAMSTAIALSHNMFDAVLYLGVCDKIVPGLLIGALHFGHLPAVFVPAGPMTSGMS 188 Query: 159 RGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGM 218 + V Q+ E + G + E EAE+ G C GTA++ ++E++G+ Sbjct: 189 NSDKVK----VRQLYAEGKIG---RTELLEAEAKSYHDAGTCTFYGTANSNQMLMEAMGL 241 Query: 219 GLPHNAAIPAVDARRQVLAHLAGR---RIVDMVREDLTMDKILTRQAFENAIRTNAAIGG 275 LP A + R L AGR +I + + + +++ ++ NAI A GG Sbjct: 242 HLPGAAFVTPNTPMRDALTAEAGRQALKITALGNQYTPVGRLVDEKSIVNAIVALLATGG 301 Query: 276 STNAVVHLIALAKRIGVELSLEDW-ELGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQ 334 STN +HL+A+AK G+ + +D+ +L + VP + + P+G + F+ AGG V+++ Sbjct: 302 STNHTLHLVAIAKAAGLIVDWDDFSKLSAVVPLITRIYPNGTADVNHFHAAGGTGFVIRE 361 Query: 335 LGEQGLLHKEALTVNGKTLWDNVRN--------------AANYDEKVITTFAEPFKPKAG 380 L + GL+H + +T+ G+ L + R A + DE V+ PF G Sbjct: 362 LLDAGLMHDDVMTILGQGLRAHCREPLLDGARPVWKDSPAESGDENVLRHAGNPFSADGG 421 Query: 381 IAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDIDEHCIMVLK 440 + +L+GNL + VIK SA + A+VF + E LD D ++ + Sbjct: 422 LKLLQGNLGRS--VIKVSAVKHEHRAVQAPAIVFHSQEAFMHAFKAGELDKDFIAVLTFQ 479 Query: 441 GAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAV--VLHVSPEAAAGG 498 G G P E+ + +LQ + ++DGRMSG A G V +HV+PE AGG Sbjct: 480 GPRANGMP---ELHALTPALGILQDKGRHVALVTDGRMSG-ASGKVPAAIHVTPEVLAGG 535 Query: 499 PLAFVQTGDMIELDVEERRLHLDVTDEELARRR 531 PL FV+TGDMI LD E L V E A R+ Sbjct: 536 PLGFVRTGDMIRLDAEAGILEALVPQEIWAARQ 568 Lambda K H 0.318 0.135 0.401 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: 872 Number of extensions: 44 Number of successful extensions: 8 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: 577 Length of database: 616 Length adjustment: 37 Effective length of query: 540 Effective length of database: 579 Effective search space: 312660 Effective search space used: 312660 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 2021. 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