Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate Ac3H11_2762 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2762 Length = 255 Score = 110 bits (276), Expect = 2e-29 Identities = 77/247 (31%), Positives = 123/247 (49%), Gaps = 5/247 (2%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGVADVSDCAQ 71 G R+LI+G A+G+G + ++ +GA V D++ + A DV+D Sbjct: 8 GRRILITGGASGMGEGLVRSLTGMGALVVSMDLNRERGEAVAKAAGARGFMEVDVADEGS 67 Query: 72 VDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAVPL 131 V R +D A ++LGGLD+LI+ AGIA P+ + A WE+ N F R P Sbjct: 68 VARAVDAACTRLGGLDVLIHAAGIA-PSSPAQGTSLALWEKVFAVNATGTFLMNRAVFPH 126 Query: 132 LKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILPGV 191 ++E + II AS AG LG ++ Y+A+K A++ +++A E GP N+RVNAI P + Sbjct: 127 MREQGGS--IINFASAAGALGLPNKSAYSAAKGAVLAWTRTVAQEWGPYNIRVNAIAPAI 184 Query: 192 VEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQNISG 251 D+ S + D + + + + D+ + FLASP + ++G Sbjct: 185 WT-PMYDQTRSEMSPEQLSAHDALMARVI-PLGGKLGDMAQDLVPVLAFLASPGARFMTG 242 Query: 252 QAISVDG 258 Q +VDG Sbjct: 243 QIFAVDG 249 Lambda K H 0.320 0.136 0.391 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: 153 Number of extensions: 7 Number of successful extensions: 4 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: 263 Length of database: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 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 (21.8 bits) S2: 47 (22.7 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