Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate 6939300 Sama_3393 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::ANA3:7024897 (256 letters) >FitnessBrowser__SB2B:6939300 Length = 241 Score = 102 bits (255), Expect = 6e-27 Identities = 74/249 (29%), Positives = 123/249 (49%), Gaps = 15/249 (6%) Query: 13 KTIFISGGATGIGACLVNAFLEQGAKVAF---VDILVEESTQL-VADLKQTQPEASVTFY 68 K + ++G + GIG + QG VA ++ E+T +ADL V+ Sbjct: 3 KRVLVTGSSRGIGKAIALRLASQGYDVAVHYHSNLTAAEATASEIADLG-----VKVSLL 57 Query: 69 HCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFF 128 D+ D AA++ I + G ++ NA ++ + +T + WD ++TNL ++ Sbjct: 58 KFDVADRAAVRAAIEADIEANGAYYGVVLNAGINRDTAFPAMTDDDWDSVIHTNLDGFYN 117 Query: 129 AVQ-AVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIR 187 VQ V P +Q GG +I L S+S G Y+ASKAG +G T+ L+ +L K KI Sbjct: 118 VVQPTVMPMIQSRKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKIT 177 Query: 188 INTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQ 247 +N + PG + T V + ++ ++ ++ PE+IAA+A FL +DD+ T Q Sbjct: 178 VNCIAPGLIE-----TDMVSEFPSEMVDQLVPMRRMGKPEEIAALAGFLMSDDAAYITRQ 232 Query: 248 NFIVDGGWI 256 V+GG + Sbjct: 233 VISVNGGML 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: 142 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: 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