Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate SMa1351 SMa1351 enolase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Smeli:SMa1351 Length = 402 Score = 180 bits (456), Expect = 7e-50 Identities = 120/390 (30%), Positives = 184/390 (47%), Gaps = 44/390 (11%) Query: 3 ITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGE---CLGPARPNAAVV 59 I A R H + T F++A +R IE DDG VGWGE G A +V Sbjct: 28 IEANRQHQSDFGRLTTFDAAILR----------IETDDGIVGWGEGKNAAGSAGSYGTLV 77 Query: 60 QAYS----GWLIGQDPRQTEKIWAVLYNALRDQ------------GQRGLSLTALSGIDI 103 + L+G+D +W +LYN +R + +RGLS+ A+S +DI Sbjct: 78 HMLNYEVGPRLVGRDAADISAVWEMLYNGVRHERAAMSGHAMPELSRRGLSIAAISAVDI 137 Query: 104 ALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHAC 163 ALWDI GK G + LLGGR + + AYA+G + ++ +++ + GF A Sbjct: 138 ALWDILGKSLGVPVWKLLGGRKADRLPAYASGGW--ESAEKIGGQLQSYLA--SGGFKAV 193 Query: 164 KIKIGF---GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFE 220 K+++G + A R+A+GP + +M+DA+ YTV +A + WFE Sbjct: 194 KMRVGAMDGAPYVSAARVRAARKALGPSVDIMVDAHGTYTVADAKRFIQLVRDCDLAWFE 253 Query: 221 EPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQ 280 EPV+ + A VRA +P+A GE+ R+ + DI QPD CGG +E Sbjct: 254 EPVIADDKAGMAEVRAAGNVPIATGESEATRFAFRDLAVLRSADIFQPDPAFCGGITEAM 313 Query: 281 KIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQA 340 +I +A+ +R+ PH+W + L AA +P ++E+ NP Sbjct: 314 RIGAIASAFNLRLAPHLWAGAPCFFSGLHICAA--------SPASFVVEYSVGANPMIHD 365 Query: 341 VLREPLEAVNGVVTIPDGPGLGIEINRDAL 370 ++ E + +G++ IPD PGLG IN L Sbjct: 366 LVEETVAVKDGMLEIPDKPGLGFTINERVL 395 Lambda K H 0.321 0.138 0.431 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: 429 Number of extensions: 16 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: 378 Length of database: 402 Length adjustment: 30 Effective length of query: 348 Effective length of database: 372 Effective search space: 129456 Effective search space used: 129456 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