Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate BWI76_RS16795 BWI76_RS16795 amino acid ABC transporter ATPase
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >FitnessBrowser__Koxy:BWI76_RS16795 Length = 240 Score = 252 bits (644), Expect = 4e-72 Identities = 134/242 (55%), Positives = 170/242 (70%), Gaps = 2/242 (0%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60 MI I N++K +GD VL S ++K EV+ + GPSGSGKST ++C+NALE +G+V V Sbjct: 1 MIHINNLHKRFGDSHVLRGISCDIKPQEVVCIIGPSGSGKSTFLRCMNALETVSEGEVEV 60 Query: 61 DGTSIADPKTDLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120 +G + D TDL K+R VGMVFQ F LFPH T+ ENL +A + + G ++ EA + +L Sbjct: 61 NGFAAHDRATDLNKMRESVGMVFQRFNLFPHKTVLENLIMAPMNLRGMARAEAVRLAEEL 120 Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 L +VGLS P LSGGQQQRVAIARALAM P +MLFDEPTSALDPE+V +VL+VM Sbjct: 121 LAKVGLSDKRDAWPSSLSGGQQQRVAIARALAMKPSIMLFDEPTSALDPELVGDVLEVMK 180 Query: 181 QLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARSDRAQHFLDK 240 LA+EGMTM+ VTHEMGFAR+VADRVIF+DQG I E+ K + F + R FL K Sbjct: 181 NLASEGMTMVIVTHEMGFAREVADRVIFIDQGIIQEEGKPAQIFS--APTNPRTAAFLSK 238 Query: 241 IL 242 +L Sbjct: 239 VL 240 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: 178 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: 244 Length of database: 240 Length adjustment: 23 Effective length of query: 221 Effective length of database: 217 Effective search space: 47957 Effective search space used: 47957 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