Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate WP_005454216.1 SACCYDRAFT_RS05065 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >NCBI__GCF_000244975.1:WP_005454216.1 Length = 614 Score = 251 bits (641), Expect = 6e-71 Identities = 189/590 (32%), Positives = 287/590 (48%), Gaps = 67/590 (11%) Query: 6 PRLRSTQWFGTNDKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAE 65 P LRS T+ +N RS + G+ D +F G+PI+ I N++++ P + H + L E Sbjct: 2 PALRSRTT--THGRNAAGARSLWRATGMTDSDF-GKPIVAIANSYTQFVPGHVHLKDLGE 58 Query: 66 HVKRGISEAGGFPVEFPVFSNGES-NLRPSAML----TRNLASMDVEEAIRGNPIDAVVL 120 V + EAGG P EF + + + S ML +R + + VE + DA+V Sbjct: 59 VVAEAVREAGGVPREFHTIAVDDGIAMGHSGMLYSLPSREIIADSVEYMANAHQADALVC 118 Query: 121 LAGCDKTTPALLMGAASCDVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGE--- 177 ++ CDK TP +L A ++P + VSGGPM GK + G A L A+ A Sbjct: 119 ISNCDKITPGMLNAAMRLNIPTVFVSGGPMEAGKAVVVD-GVAHAPTDLITAIAASANSA 177 Query: 178 IDVHHFLSAEAGMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMS 237 +D E + G+C+ M TA++M C+ EALG++LP N + A + R L + Sbjct: 178 VDDAGLSVVEQSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARRELFTEA 237 Query: 238 GIRIVEMAL-------EGLVLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVP 290 G +VE+A E + I T+ AFENA+ + A+GGSTN V+H+ A A + Sbjct: 238 GRTVVELAKRWYGEDDESALPRSIATKQAFENAMALDMAMGGSTNTVLHILAAAREGEID 297 Query: 291 LELEDWMRIGRDTPTIVDLMPSGRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGK 350 L+D RIGR+ P + + P+ + ME+ + AGG+PA+L L GG L N D +V+ Sbjct: 298 FTLDDIDRIGREVPCLSKVSPNSDYHMEDVHRAGGIPAILGELHRGGFL-NTDVHSVHSS 356 Query: 351 SL------WD-------------------NVREAPNYDEE-------------VIRPLDR 372 SL WD VR + +R ++ Sbjct: 357 SLEEWLSTWDIRGGSPSERALELFHAAPGGVRTTEAFSTSNRWSSLDTDAANGCVRDVEH 416 Query: 373 PLIADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDA 432 A GG+ +LRGNLA GAV+K + EL + RG A V E+ + + I ++ ++ + Sbjct: 417 AYTASGGLTVLRGNLAENGAVIKSAGIDEELWRFRGPARVVESQEEAVSAILNK--EVRS 474 Query: 433 SSVMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGV---KDMVRISDARMSGTAYGTVVLHV 489 V+V++ GP G PGM E+ L P +G K I+D R SG + G V H+ Sbjct: 475 GEVIVVRYEGPAGGPGMQEM----LHPTAFLKGAGLGKVCALITDGRFSGGSSGISVGHI 530 Query: 490 APEAAAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAP 539 +PEAAAGG + V NGD I +D L L + + L R + ++ + P Sbjct: 531 SPEAAAGGTIGLVENGDEILIDVHERKLELLVDAEVLAERRAKMEASERP 580 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: 929 Number of extensions: 59 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 583 Length of database: 614 Length adjustment: 37 Effective length of query: 546 Effective length of database: 577 Effective search space: 315042 Effective search space used: 315042 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 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