Align 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43) (characterized)
to candidate HSERO_RS19330 HSERO_RS19330 FAH family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_611 (330 letters) >FitnessBrowser__HerbieS:HSERO_RS19330 Length = 331 Score = 412 bits (1059), Expect = e-120 Identities = 199/331 (60%), Positives = 242/331 (73%), Gaps = 1/331 (0%) Query: 1 MRLVQFELPNGERRVGVVDGDQVREVQGAASVRDLALAAIEAGVKLEEQVNSLGLGAGHD 60 +RL+Q+ GERRVG+V+G Q++ + A++R+LAL A++ G+ LE Q L D Sbjct: 1 VRLIQYRDRAGERRVGIVNGGQIQALDQVATMRELALLALQRGIGLERQAQLLNTDRCED 60 Query: 61 YARLLSELRILPPLDHPDPAHLLVSGTGLTHLGSASARDKMHQQA-GDESAMTDTMRIFK 119 YA +L+E RIL PLDHPDPAH +SG G THLGSA+ RDKMH++ GDE TDT + + Sbjct: 61 YAAILAEGRILAPLDHPDPAHCRISGAGTTHLGSATTRDKMHRRIEGDELDKTDTQLMIE 120 Query: 120 WGVEGGKPQAGQAGVQPEWFYKGDGSIVVRPGHPFPLPPFAEDAGEEPEISGLYVIGHDG 179 WG+ GG+P AG+AGVQPEWFYKGDGS +V PG P P FA D GEEPEI GLY+I +G Sbjct: 121 WGIAGGRPAAGEAGVQPEWFYKGDGSSIVAPGAALPRPDFALDGGEEPEIVGLYLIDEEG 180 Query: 180 KPYRLGFAVGNEFSDHVMERKNYLYLAHSKLRSCSFGPELRVGELPQHLSGTSRILRNGE 239 P RLGFA+GNEFSDHVMER+NYLY HSKLR CSFGPEL VG P HL G +RI RNG Sbjct: 181 CPRRLGFAIGNEFSDHVMERRNYLYQGHSKLRHCSFGPELLVGLPPAHLVGMTRIRRNGR 240 Query: 240 VLWQNEFLSGEANMCHSLENLEFHHFKYSQFLRPGDVHVHFFGTATLSFADGIRTQPGDV 299 V+W+ EFL+G NMCHS+ENLE+H+FKYS L GDVHVH+ G A LSFA +RT+ GD Sbjct: 241 VIWEQEFLTGPDNMCHSIENLEYHYFKYSHLLHAGDVHVHYMGAANLSFAYSVRTEDGDS 300 Query: 300 FEISQAEFGAPLVNGIAPVDAVFNPGTIGTL 330 EIS +FGAPLVNGIA V + F PG + L Sbjct: 301 IEISIPDFGAPLVNGIAHVKSAFRPGGVKPL 331 Lambda K H 0.319 0.139 0.422 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: 402 Number of extensions: 13 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: 331 Length adjustment: 28 Effective length of query: 302 Effective length of database: 303 Effective search space: 91506 Effective search space used: 91506 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