Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_955 Length = 619 Score = 197 bits (501), Expect = 1e-54 Identities = 169/534 (31%), Positives = 257/534 (48%), Gaps = 76/534 (14%) Query: 120 DGRTQGTTGMFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNI 179 DG G GM SLP R+ + + ++ + A A++ +++CDK P +MA A + NI Sbjct: 81 DGIAMGHDGMLYSLPSRDIIADSVEYMVNA-HCADAMVCISNCDKITPGMLMA-AMRLNI 138 Query: 180 ATVLVPGGATLPAKDGEDNG--------KVQTIGARFANGELSLQDA-----RRAGCKAC 226 + V GG K N K+ + A + + DA R+ C C Sbjct: 139 PVIFVSGGPMEAGKTRLANPVTKVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTC 198 Query: 227 ASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQK--- 283 G C + TA + + E LGL++P + + ++ + + R ++L+++ Sbjct: 199 ----GSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYE 254 Query: 284 ----GITTREILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIP-TVDDWIRINK 338 + R + KA ENAMT+ A GGSTN +LH+ AIA +A IP T+ D R+++ Sbjct: 255 QDDERVLPRSV-GFKAFENAMTLDIAMGGSTNTILHLLAIASEA--EIPFTMADIDRLSR 311 Query: 339 RVPRLVSVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWE 398 VP+L V PN YH + AGG+ ++ L G LH DV TV +TLK+ LD W+ Sbjct: 312 VVPQLCKVAPNTNKYH-IEDVHRAGGIMAILGELDRAGKLHTDVPTVHTATLKDALDQWD 370 Query: 399 ------------------------HSERRQRFKQLLLDQEQINADEVIMSPQQAKAR-GL 433 + R+ L LD+ A+ I S A ++ G Sbjct: 371 IVRTQDEAVRTFYMAGPAGVPTQVAFSQATRWPSLDLDR----AEGCIRSYDHAFSKEGG 426 Query: 434 TSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKA 493 + +T GNIA +G V+KS +D S I +G A V S+ A+ +I DK++A Sbjct: 427 LAVLT---GNIAVDGCVVKSAGVDES------ILVFEGTAHVTESQDEAVANILADKVQA 477 Query: 494 GDILVIIGVGP-SGTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEA 552 GD++++ GP G GM+E TS +K GK +L+TD RFSG ++G IGH PEA Sbjct: 478 GDVVIVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEA 537 Query: 553 LAGGPIGKLRTGDLIEIKIDCRELHGEVNFLGTRSDEQLPSQEEATAILNARPS 606 AGG IG ++ GD I I I R ++ V SDE+L + EA +P+ Sbjct: 538 AAGGAIGLVQNGDRIRIDIPNRTINVLV------SDEELAKRREAQNAKGWKPA 585 Lambda K H 0.317 0.135 0.400 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: 882 Number of extensions: 36 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: 655 Length of database: 619 Length adjustment: 38 Effective length of query: 617 Effective length of database: 581 Effective search space: 358477 Effective search space used: 358477 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: 54 (25.4 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