Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate 8500099 DvMF_0862 ABC transporter related (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Miya:8500099 Length = 248 Score = 290 bits (743), Expect = 1e-83 Identities = 142/244 (58%), Positives = 188/244 (77%) Query: 10 SPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69 S E II++ K++G+ L D++L+V GE++V+CGPSGSGKST +R +NRLE +G Sbjct: 5 SVEPIIRISHAWKFFGELTALNDVSLDVMPGEKVVICGPSGSGKSTLLRSINRLETVDKG 64 Query: 70 RIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEI 129 I+VDG ++ + I IR+E+GMVFQ FNLFPH T+LQN T+APM +RK P+ +AE Sbjct: 65 TIIVDGQDVNSPDNDINKIRQELGMVFQSFNLFPHKTVLQNLTMAPMRLRKTPRAEAESR 124 Query: 130 AMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVL 189 A+ L++V I ++A+ +P LSGGQQQRVAIARAL M PKIMLFDEPTSALDPEM+ EVL Sbjct: 125 ALELLKKVGISDKANVFPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVL 184 Query: 190 DTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFL 249 D M+ LA +GMTM+CVTHEMGFAR VA+R+IFMD G+++E+ AP DFF P++ R + FL Sbjct: 185 DVMVTLAREGMTMVCVTHEMGFAREVADRIIFMDHGQVLEENAPQDFFGAPKHPRLQKFL 244 Query: 250 SQIL 253 +QIL Sbjct: 245 NQIL 248 Lambda K H 0.322 0.137 0.407 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: 217 Number of extensions: 6 Number of successful extensions: 1 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: 254 Length of database: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 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 (21.9 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