Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__HerbieS:HSERO_RS16705 Length = 578 Score = 754 bits (1946), Expect = 0.0 Identities = 369/571 (64%), Positives = 453/571 (79%), Gaps = 6/571 (1%) Query: 12 RSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVK 71 RSQ W+G RD +R W+KN+G PHD FDGRPVIGI NT+S++TPCN H R LAE+VK Sbjct: 11 RSQAWFGRQDRDGFIYRSWVKNRGIPHDQFDGRPVIGICNTYSELTPCNSHFRALAEQVK 70 Query: 72 AGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTT 131 G+WEAGGFPLE PV S E RPTAM+YRNLA++ VEE+IR P+DG VLL+GCDKTT Sbjct: 71 IGIWEAGGFPLEFPVMSLGETLLRPTAMLYRNLASMDVEESIRANPLDGVVLLMGCDKTT 130 Query: 132 PSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEA 191 P+LLMGAAS D+P+I V+GGPML+G +RG +GSGT +W+ SE V+AG+MTQ EF EAE+ Sbjct: 131 PALLMGAASVDVPTIGVSGGPMLSGKYRGRELGSGTGVWQMSEDVRAGKMTQEEFFEAES 190 Query: 192 SMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD 251 M RS G C TMGTASTMASM EALG+ L NAAIP VD+RR V+A+ GRRIVQMV++D Sbjct: 191 CMHRSHGHCMTMGTASTMASMVEALGVGLPHNAAIPAVDARRNVLARNAGRRIVQMVEED 250 Query: 252 LKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVN 311 L S+I+T+QAFENAIR NAAIGGSTNAVIHLLAIAGR+GI L L DWD G+ +P +++ Sbjct: 251 LVLSKILTRQAFENAIRVNAAIGGSTNAVIHLLAIAGRIGIKLDLKDWDDIGQQLPCLLD 310 Query: 312 LMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILP 371 L PSGK+LME+F+YAGGLP V+++L ++ K ALT +G+T+W+ +D NWNE+VI Sbjct: 311 LQPSGKFLMEDFYYAGGLPAVIRQL--ESVIDKTALTANGKTLWENCQDAPNWNEEVIRS 368 Query: 372 AEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLD 431 +K + GI +L+GNLAP GAV+KPSAA+P LL H+GRAVVFE+ DD +I+D+NLD Sbjct: 369 FDKPFKEAAGIAILKGNLAPDGAVIKPSAATPALLKHRGRAVVFENSDDLHKRIDDENLD 428 Query: 432 IDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHT 491 +DE C++V+KNCGPKGYPGMAE GNM LPPK+L+KGI DMVR+SDARMSGTAYGTVVLH Sbjct: 429 VDETCVLVLKNCGPKGYPGMAEAGNMPLPPKILRKGITDMVRVSDARMSGTAYGTVVLHV 488 Query: 492 SPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTS---GYAF 548 SPEAA GGPLAVV+NGD IELDV R+LHLD+SDEELARR A+WQ +LP G+ Sbjct: 489 SPEAAAGGPLAVVQNGDFIELDVEARKLHLDVSDEELARRRAQWQ-KPELPPQMQRGWVK 547 Query: 549 LHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579 L+ HV+ A+ GADLDFL G G V KD+H Sbjct: 548 LYVDHVQQANQGADLDFLVGKSGPYVPKDNH 578 Lambda K H 0.318 0.135 0.408 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: 1131 Number of extensions: 54 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: 579 Length of database: 578 Length adjustment: 36 Effective length of query: 543 Effective length of database: 542 Effective search space: 294306 Effective search space used: 294306 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 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