Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate SMa1351 SMa1351 enolase
Query= curated2:A9BQY2 (395 letters) >FitnessBrowser__Smeli:SMa1351 Length = 402 Score = 137 bits (345), Expect = 5e-37 Identities = 119/375 (31%), Positives = 170/375 (45%), Gaps = 51/375 (13%) Query: 46 RQSRRSFG-INVLGTLVVEIEDSAGRVGFAV--TTGGEPAAYIVEKHLARFLEGARVT-- 100 RQ + FG + ++ IE G VG+ G +Y H+ + G R+ Sbjct: 32 RQHQSDFGRLTTFDAAILRIETDDGIVGWGEGKNAAGSAGSYGTLVHMLNYEVGPRLVGR 91 Query: 101 ---DIERIWDQMYLSTLY------------YGRKGIVINTISGVDLALWDLLGKVRGEPV 145 DI +W+ +Y + R+G+ I IS VD+ALWD+LGK G PV Sbjct: 92 DAADISAVWEMLYNGVRHERAAMSGHAMPELSRRGLSIAAISAVDIALWDILGKSLGVPV 151 Query: 146 HQLLGGAVRDELQFYATGARPDLAQKMG-------FIGG--KMPLHHGPAEGEEGLRRNL 196 +LLGG D L YA+G + A+K+G GG + + G +G + + Sbjct: 152 WKLLGGRKADRLPAYASGGW-ESAEKIGGQLQSYLASGGFKAVKMRVGAMDGAPYV--SA 208 Query: 197 QELATMRERVGPDFWLMLDCWMSLDVNYATRLAQGAQAHGLKWIEEALPPDDYWGYAALR 256 + R+ +GP +M+D + V A R Q + L W EE + DD G A +R Sbjct: 209 ARVRAARKALGPSVDIMVDAHGTYTVADAKRFIQLVRDCDLAWFEEPVIADDKAGMAEVR 268 Query: 257 K--NVPTGMLVTTGEHEATRWGFRQLLEMGCCDIIQPDVGWCGGITELLKISALADAHQA 314 NVP + TGE EATR+ FR L + DI QPD +CGGITE ++I A+A A Sbjct: 269 AAGNVP----IATGESEATRFAFRDLAVLRSADIFQPDPAFCGGITEAMRIGAIASAFNL 324 Query: 315 LVIPH---GSSVY--SYHFVATRHNSPFAEFLMMAPKADEVVPMFHPQLLGEPVPVNGRM 369 + PH G+ + H A S E+ + A PM H L+ E V V M Sbjct: 325 RLAPHLWAGAPCFFSGLHICAASPASFVVEYSVGAN------PMIH-DLVEETVAVKDGM 377 Query: 370 RLSALDRPGFGVELN 384 L D+PG G +N Sbjct: 378 -LEIPDKPGLGFTIN 391 Lambda K H 0.322 0.139 0.442 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: 431 Number of extensions: 20 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: 395 Length of database: 402 Length adjustment: 31 Effective length of query: 364 Effective length of database: 371 Effective search space: 135044 Effective search space used: 135044 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 (21.9 bits) S2: 50 (23.9 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