Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_012333306.1 M446_RS16850 phosphogluconate dehydratase
Query= reanno::WCS417:GFF2156 (578 letters) >NCBI__GCF_000019365.1:WP_012333306.1 Length = 616 Score = 191 bits (486), Expect = 6e-53 Identities = 155/510 (30%), Positives = 238/510 (46%), Gaps = 37/510 (7%) Query: 61 RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL 120 R+ A + AGG P + GE+ + ++ +R++ ++ A+ D V Sbjct: 101 REAAREAGGVALVAGGVPAMCDGITQGEAGME-LSLFSRDVIALSTAVALSHQTFDAAVF 159 Query: 121 LTGCDKTTPALLMGA-ASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTIT 179 L CDK P L++GA A +PA+ + GPM +G + ++ + G + Sbjct: 160 LGICDKIVPGLVIGALAFGHLPAVFIPSGPMTSGLPNPEKA-------KIRQLYAEGKVG 212 Query: 180 LDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGM 239 D LAAE GTC GTA+T + E +G LP + + R L + Sbjct: 213 RDALLAAESDSYHGPGTCTFYGTANTNQMLMEMMGLHLPGASFVTPDTPLRDALTRAAAQ 272 Query: 240 RAVEMV---REDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDW 296 RA+ + E L + ++L + AF N I A GGSTN +HL +A G+ L +D Sbjct: 273 RALAITALGNEYLPVGQLLDERAFANGIVGLHATGGSTNHTLHLLPMAAAAGITLTWEDL 332 Query: 297 TRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRR-LGEANLIPHPNALTVNGKSLGEN 355 + + P + + P+G + F+ AGG+P V+R LGE L H +A TV G L Sbjct: 333 SDLAEVTPLLARVYPNGTADVNHFHAAGGMPFVIRELLGEGLL--HADAQTVLGAGLHAY 390 Query: 356 TQDSPI--------------YGQDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAAS 401 T++ + G+ V+R P + GG+ VL GNL AV+K SA + Sbjct: 391 TREPVLTEAGGLAWREGPAESGETGVLRGAAAPFQPTGGLAVLAGNLG--RAVIKTSAVA 448 Query: 402 PALMQHRGRAVVFENFDMYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAK 461 P A VF + + +A EL D + V++ GPK GM E+ + P Sbjct: 449 PERQVIEAPARVFHSQEALQAAFRAGELRGDV--VAVVRFQGPKA-NGMPELHKLMPPLG 505 Query: 462 LLAQGVTDMVRISDARMSGTAYGTV--VLHVAPEAAAGGPLATVKEGDWIELDCANGRLH 519 +L + ++D R+SG A G V +HV PEAA GGP+A +++GD + +D GRL Sbjct: 506 VLQDRGHRVALVTDGRLSG-ASGKVPSAIHVTPEAAEGGPIARIRDGDVVRVDAPAGRLE 564 Query: 520 LDIPDAELAARMADLAPPQKLIVGGYRQLY 549 + +P AE AAR A VG R+L+ Sbjct: 565 VLVPPAEWAARAPATADLAASHVGIGRELF 594 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: 956 Number of extensions: 68 Number of successful extensions: 5 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: 616 Length adjustment: 37 Effective length of query: 541 Effective length of database: 579 Effective search space: 313239 Effective search space used: 313239 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 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