Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)
Query= reanno::ANA3:7024897 (256 letters) >FitnessBrowser__Btheta:353297 Length = 248 Score = 135 bits (341), Expect = 6e-37 Identities = 82/250 (32%), Positives = 131/250 (52%), Gaps = 13/250 (5%) Query: 10 LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEA---SVT 66 L GKT ++G A GIG + F +GA +AF D++++E+ A+ + + EA Sbjct: 4 LDGKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDEN----AEKTRVELEAMGVKAK 59 Query: 67 FYHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHY 126 Y + + +V+ ++ D G I +L+NNA + + ++ + WD +N NL+ Sbjct: 60 GYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSA 119 Query: 127 FFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKI 186 F + A P M R GS+IN+ S+ + AG A Y ASKAG + L + +A +LG I Sbjct: 120 FNFIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGI 179 Query: 187 RINTLTPGWVMT--KRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLC 244 R N + PG+++T L+ V + AK I ++ PED+A +A FLA+D S Sbjct: 180 RANAIAPGFILTDMTAALSDEVRAEWAKKIP----LRRGGTPEDVANIATFLASDMSSYV 235 Query: 245 TAQNFIVDGG 254 + Q VDGG Sbjct: 236 SGQVIQVDGG 245 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: 136 Number of extensions: 6 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: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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