Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate BWI76_RS10275 BWI76_RS10275 ABC transporter
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >FitnessBrowser__Koxy:BWI76_RS10275 Length = 246 Score = 243 bits (621), Expect = 2e-69 Identities = 125/243 (51%), Positives = 173/243 (71%), Gaps = 4/243 (1%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60 ++ + ++K +G VL +CS EV++GE +V+ GPSGSGKSTL++CVN L P GDV Sbjct: 6 LLEMIGIDKTFGRQTVLKNCSLEVQRGETVVLIGPSGSGKSTLLRCVNMLSPADSGDVFF 65 Query: 61 DGTSIADPKTDLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120 I+ + + KLR R+GMVFQ++ELF HLT EN+ +A + VLG ++ +A L Sbjct: 66 ASQHISRGEVPVHKLRQRIGMVFQNYELFSHLTAAENIMLAPMTVLGMNRTDARTLADNL 125 Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 L +V ++ A P +LSGGQQQRVAIARALAM P +ML+DEPTSALDPEM+ EVL+VM Sbjct: 126 LAKVRINERADHFPDELSGGQQQRVAIARALAMKPELMLYDEPTSALDPEMIREVLEVMA 185 Query: 181 QLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFF-GDINARSDRAQHFLD 239 +L+ EGMT M VTHEMGFAR+ A++++FM+ G+II+ +FF G++ S+RAQ FL Sbjct: 186 ELSAEGMTSMVVTHEMGFARRAANKILFMEDGEIIDRASTSDFFAGNV---SERAQRFLT 242 Query: 240 KIL 242 +IL Sbjct: 243 QIL 245 Lambda K H 0.321 0.136 0.394 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: 190 Number of extensions: 5 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: 244 Length of database: 246 Length adjustment: 24 Effective length of query: 220 Effective length of database: 222 Effective search space: 48840 Effective search space used: 48840 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