Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate WP_011384917.1 AMB_RS12770 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >NCBI__GCF_000009985.1:WP_011384917.1 Length = 616 Score = 229 bits (585), Expect = 2e-64 Identities = 176/568 (30%), Positives = 281/568 (49%), Gaps = 63/568 (11%) Query: 16 TNDKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAG 75 T+ +N R + G+ D +F G+PII I N++++ P + H + L + V R I +AG Sbjct: 10 THGRNMSGARGLWRATGMTDADF-GKPIIAIANSFTQFVPGHVHLKDLGQMVAREIEKAG 68 Query: 76 GFPVEFPVFSNGESNLRPSAML-----TRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPA 130 G EF + + A + +R L + VE + + DA+V ++ CDK TP Sbjct: 69 GVAKEFDTIAIDDGIAMGHAGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPG 128 Query: 131 LLMGAASCDVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGEIDV--HHFLSAEA 188 +LM + ++P I +SGGPM GK+ + G AV + +K + +V L+ E Sbjct: 129 MLMASLRLNIPTIFISGGPMEAGKVTYQ--GETHAVDLIDAMIKGADQNVSDEEALAFEK 186 Query: 189 GMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEM---A 245 + G+C+ M TA++M C+ EALG+ LP N + A + R L +G RIV++ A Sbjct: 187 ESCPTCGSCSGMFTANSMNCLIEALGLGLPGNGTVVATHADRKELFLEAGRRIVDLARRA 246 Query: 246 LEG----LVLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIGR 301 EG ++ I T AFENA+ + A+GGSTN V+HL A A GV + D R+ R Sbjct: 247 YEGDDASVLPRSIATFQAFENAMTLDIAMGGSTNTVLHLLAAAQEAGVAFGMSDIDRLSR 306 Query: 302 DTPTIVDLMPS-GRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSL------WD 354 P + + P+ +E+ + AGG+ +L +L GGL+ N + T++ ++L WD Sbjct: 307 RVPCLCKVAPNVPDVHIEDVHRAGGIMGILGQLDRGGLI-NRECGTIHARTLAEGLDRWD 365 Query: 355 ------------------NVREAPNYDEE-------------VIRPLDRPLIADGGIRIL 383 VR + + VIR +D DGG+ +L Sbjct: 366 ISRSNDPKVVEFYKAAPGGVRTTEAFSQSKRWAEVDKDRTAGVIRSVDNAFSKDGGLAVL 425 Query: 384 RGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSVMVLKNCGP 443 GNLA G ++K + + L G AV+ E+ D A I + + V++++ GP Sbjct: 426 FGNLALDGCIVKTAGVDDKNLTFSGPAVICESQDEAVAKILGG--QVKSGDVVIVRYEGP 483 Query: 444 RGYPGMAEVGNMGLPPKLLR-QGV-KDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLAA 501 RG PGM E M P L+ G+ K+ I+D R SG G + HV+PEAA GG + Sbjct: 484 RGGPGMQE---MLYPTSYLKSMGLGKECALITDGRFSGGTSGLSIGHVSPEAAEGGAIGL 540 Query: 502 VRNGDWIELDCEAGTLHLDITDDELHRR 529 ++ GD I++ ++ + ++D EL +R Sbjct: 541 IQAGDIIDIHIPNRSIAIRVSDAELEKR 568 Lambda K H 0.319 0.136 0.412 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: 886 Number of extensions: 44 Number of successful extensions: 7 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: 583 Length of database: 616 Length adjustment: 37 Effective length of query: 546 Effective length of database: 579 Effective search space: 316134 Effective search space used: 316134 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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