Align 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) (characterized)
to candidate GFF2158 PS417_11010 FAH family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_4623 (330 letters) >FitnessBrowser__WCS417:GFF2158 Length = 329 Score = 578 bits (1489), Expect = e-170 Identities = 281/330 (85%), Positives = 302/330 (91%), Gaps = 1/330 (0%) Query: 1 MRLVQFELSHGERRVGVVEDGLVREVRDARSVRDLALAAIEAGVNLEQQVQTLGLGISHD 60 MRLVQFELS+GERRVGVVE +REV+ ARSVR+LALAAIEAGV L QQV LGLG SHD Sbjct: 1 MRLVQFELSNGERRVGVVEGDSLREVQTARSVRELALAAIEAGVGLAQQVNNLGLGDSHD 60 Query: 61 YSALLANLQILPPLDHPDPAHMLVSGTGLTHLGSASARDKMHQQAGDETAMTDTMRIFKW 120 Y+ LLA L+ILPPLDHPDPAHML+SGTGLTHLGSASARDKMHQ AGD+TA+TDTMRIFKW Sbjct: 61 YATLLAGLKILPPLDHPDPAHMLISGTGLTHLGSASARDKMHQ-AGDDTALTDTMRIFKW 119 Query: 121 GVEGGKPATGQVGVQPEWFYKGDGSIVVRPGKPFPLPPFAEDAGEEPELSGLYVIGHDGK 180 GVEGGKPA GQ GVQPEWFYKGDGS VVRPG FP+PPFAEDAGEEPE+ GLYVIG D K Sbjct: 120 GVEGGKPAAGQAGVQPEWFYKGDGSNVVRPGAAFPVPPFAEDAGEEPEIGGLYVIGPDSK 179 Query: 181 PYRLGFAVGNEFSDHVMERKNYLYLAHSKLRSCSYGPELRVGELPQHLAGTSRILRDGEV 240 PYR+GFAVGNEFSDHVMERKNYLYLAHSKLRSCSYGPELRVGELPQHLAGTSRI+R+GE Sbjct: 180 PYRVGFAVGNEFSDHVMERKNYLYLAHSKLRSCSYGPELRVGELPQHLAGTSRIVRNGEE 239 Query: 241 LWQNEFLSGEANMCHSLENLEYHHFKYSQFLRPGDVHIHFFGTATLSFADGIRTQPGDVF 300 +W+NEFLSGEANMCHSLENLEYHHFKY QFL+PGDVHIHFFGTATLSFADGIRTQPGDVF Sbjct: 240 IWRNEFLSGEANMCHSLENLEYHHFKYRQFLKPGDVHIHFFGTATLSFADGIRTQPGDVF 299 Query: 301 EISQAEFGAPLINGIEPVEAAFEPGTVGTL 330 EISQA+FGAPL+N + +AAFEPG V TL Sbjct: 300 EISQADFGAPLVNRVGSSDAAFEPGNVITL 329 Lambda K H 0.319 0.138 0.419 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: 552 Number of extensions: 18 Number of successful extensions: 2 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: 330 Length of database: 329 Length adjustment: 28 Effective length of query: 302 Effective length of database: 301 Effective search space: 90902 Effective search space used: 90902 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: 49 (23.5 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