Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate H281DRAFT_03637 H281DRAFT_03637 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= reanno::ANA3:7024897 (256 letters) >FitnessBrowser__Burk376:H281DRAFT_03637 Length = 255 Score = 130 bits (328), Expect = 2e-35 Identities = 78/250 (31%), Positives = 132/250 (52%), Gaps = 6/250 (2%) Query: 9 SLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFY 68 +L G+ + ++GGA G+GA V A ++ GA+V F D+L EE L A L Q A++ + Sbjct: 8 TLNGRRVLVTGGARGLGAAFVRALVQAGAQVVFGDVLHEEGRALAASL-AGQGHAAI-YL 65 Query: 69 HCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHS--IDEVTPEYWDQCLNTNLRHY 126 DL D ++K+ Q LG I LINNAA DE++ + WD +N N+R Sbjct: 66 PLDLADPESIKQFAEQGASRLGGIDALINNAAITNSGGKFADELSVDTWDAVMNVNVRGT 125 Query: 127 FFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKI 186 + AV P ++ G GS++N+ S + + Y ASK + +TR LA + G ++ Sbjct: 126 WLMSTAVLPYLRDSGRGSIVNIASDTAMWGAPKLLAYVASKGAVISMTRSLAREFGAHQV 185 Query: 187 RINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTA 246 +N + PG +T+ + T +V + ++ + + +P+D+ LFL +D ++ T Sbjct: 186 TVNAIAPG--LTEVEATAYVPAERHEYYLQGRALTRAQVPDDVTGPVLFLLSDAARFVTG 243 Query: 247 QNFIVDGGWI 256 Q V+GG++ Sbjct: 244 QLLPVNGGFV 253 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: 143 Number of extensions: 12 Number of successful extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 Effective search space: 53592 Effective search space used: 53592 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