Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate BWI76_RS10275 BWI76_RS10275 ABC transporter
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__Koxy:BWI76_RS10275 Length = 246 Score = 247 bits (630), Expect = 2e-70 Identities = 121/246 (49%), Positives = 176/246 (71%) Query: 9 VSPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQ 68 +S + +++M G++K +G+ VLK+ +L V++GE +VL GPSGSGKST +RC+N L Sbjct: 1 MSEKPLLEMIGIDKTFGRQTVLKNCSLEVQRGETVVLIGPSGSGKSTLLRCVNMLSPADS 60 Query: 69 GRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEE 128 G + ++ + +R+ +GMVFQ++ LF HLT +N LAPM V M + A Sbjct: 61 GDVFFASQHISRGEVPVHKLRQRIGMVFQNYELFSHLTAAENIMLAPMTVLGMNRTDART 120 Query: 129 IAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEV 188 +A + L +VRI E+A +P +LSGGQQQRVAIARAL MKP++ML+DEPTSALDPEM++EV Sbjct: 121 LADNLLAKVRINERADHFPDELSGGQQQRVAIARALAMKPELMLYDEPTSALDPEMIREV 180 Query: 189 LDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLF 248 L+ M L+ +GMT + VTHEMGFAR AN+++FM+ GEI+++A+ +DFF ++R + F Sbjct: 181 LEVMAELSAEGMTSMVVTHEMGFARRAANKILFMEDGEIIDRASTSDFFAGNVSERAQRF 240 Query: 249 LSQILH 254 L+QILH Sbjct: 241 LTQILH 246 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: 177 Number of extensions: 4 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: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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