Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_111391131.1 CLV31_RS01670 SDR family oxidoreductase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_003253485.1:WP_111391131.1 Length = 256 Score = 107 bits (268), Expect = 2e-28 Identities = 76/252 (30%), Positives = 121/252 (48%), Gaps = 13/252 (5%) Query: 10 LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYH 69 LQ K I ISGGA GIG + +E+GA +D +E +LV + Sbjct: 5 LQDKVILISGGAKGIGGAISKGLIEEGAIPVIIDPSEKEGKELVELAVGKALHLPWRLFS 64 Query: 70 CDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFA 129 + + A L+ V A G I ++NNA + +++ +PE + Q + NL HY+ Sbjct: 65 AEDCEKAVLEAVRA-----FGRIDGVVNNAGANDGVGLEKGSPEAFAQSIANNLHHYYSL 119 Query: 130 VQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRIN 189 V P++++ G+++N+ S + Q G +GY A+K + LTR + +L IR+N Sbjct: 120 VHFALPELKK-SQGAIVNISSKTAVTGQGGTSGYVAAKGAQLALTREWSVELLPYHIRVN 178 Query: 190 TLTPGWVMTKRQLTHWVD---KDTAKHIENNQCI---KEYVMPEDIAAMALFLAADDSKL 243 + P V T W+ K E N I K PE+IA+MA+FL ++ + Sbjct: 179 AILPAEVYTP-MYESWIQTFPNPEEKLAEINHQIPLGKRMTTPEEIASMAIFLLSNRASH 237 Query: 244 CTAQNFIVDGGW 255 T Q+ VDGG+ Sbjct: 238 ITGQHLYVDGGY 249 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: 166 Number of extensions: 11 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: 256 Length of database: 256 Length adjustment: 24 Effective length of query: 232 Effective length of database: 232 Effective search space: 53824 Effective search space used: 53824 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 24 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