Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate WP_007695653.1 C447_RS15655 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >NCBI__GCF_000336675.1:WP_007695653.1 Length = 332 Score = 141 bits (355), Expect = 2e-38 Identities = 89/224 (39%), Positives = 131/224 (58%), Gaps = 15/224 (6%) Query: 1 MISIKNVNKWYGDFQVLTDCST-EVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVV 59 MI NV+K Y D D EV++G V+ GPSG GK+T ++ VN LE +G + Sbjct: 1 MIRFDNVHKQYPDGTRAVDGHDFEVEEGTTTVLVGPSGCGKTTTMRLVNRLEEPTEGTIY 60 Query: 60 VDGTSIADPKTDLPKLRSRVGMVFQHFELFPHLTITENL-TIAQIKVLGRSKEEATKKGL 118 DGT I + + LR +G V Q LF H+T+ EN+ T+ ++K G E + Sbjct: 61 YDGTDIEE--LEATDLRREIGYVIQDIGLFDHMTVGENVATVPELK--GWEAERTADRVD 116 Query: 119 QLLERVGLSAHAHK--HPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP----EMV 172 +LLE +GL + +PG+LSGGQQQRV +ARALA P VML DEP ALDP E+ Sbjct: 117 ELLELMGLPPEEFRDSYPGELSGGQQQRVGVARALAAGPDVMLMDEPFGALDPITREELQ 176 Query: 173 NEVLDVMVQLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIE 216 +E LD+ ++ T++ VTH++ A K+ D++ M++GK+++ Sbjct: 177 DEFLDIQKEI---DTTIVFVTHDINEALKMGDKIAVMNEGKVVQ 217 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: 203 Number of extensions: 10 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: 244 Length of database: 332 Length adjustment: 26 Effective length of query: 218 Effective length of database: 306 Effective search space: 66708 Effective search space used: 66708 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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