Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate 7023089 Shewana3_0327 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::ANA3:7024897 (256 letters) >FitnessBrowser__ANA3:7023089 Length = 241 Score = 100 bits (249), Expect = 3e-26 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 13/246 (5%) Query: 15 IFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEA---SVTFYHCD 71 + ++G + GIG + G +A L S Q AD + A +V+ D Sbjct: 5 VLVTGSSRGIGKAIALKLAAAGYDIA----LHYHSNQAAADASAAELSALGVNVSLLKFD 60 Query: 72 LVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFAVQ 131 + D AA+K I + G +I NA ++ ++ ++ WD ++TNL ++ + Sbjct: 61 VADRAAVKAAIEADIEANGAYYGVILNAGINRDNAFPAMSEAEWDSVIHTNLDGFYNVIH 120 Query: 132 -AVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRINT 190 V P +Q GG +I L S+S G Y+ASKAG +G T+ L+ +L K KI +N Sbjct: 121 PCVMPMVQGRKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVNC 180 Query: 191 LTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQNFI 250 + PG + T + + KD +E ++ P +IAA+A FL +DD+ T Q Sbjct: 181 IAPGLIET--DMVADIPKDM---VEQLVPMRRMGKPNEIAALAAFLMSDDAAYITRQVIS 235 Query: 251 VDGGWI 256 V+GG I Sbjct: 236 VNGGMI 241 Lambda K H 0.320 0.134 0.406 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: 135 Number of extensions: 7 Number of successful extensions: 3 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: 256 Length of database: 241 Length adjustment: 24 Effective length of query: 232 Effective length of database: 217 Effective search space: 50344 Effective search space used: 50344 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: 46 (22.3 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