Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_007501456.1 BA79_RS06410 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >NCBI__GCF_000691145.1:WP_007501456.1 Length = 242 Score = 277 bits (709), Expect = 1e-79 Identities = 137/244 (56%), Positives = 180/244 (73%), Gaps = 2/244 (0%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60 MI+ + VNK YG F VL D + ++KGEV+V+ GPSGSGKST+++C+N LE +G V+V Sbjct: 1 MITFEEVNKHYGQFHVLKDINLHIQKGEVVVIIGPSGSGKSTMLRCINRLESIDEGKVLV 60 Query: 61 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQL 120 + S+ PKTN+ +R +GMVFQHF L+PH ++++N+ +A +KV SKEEA + A Sbjct: 61 NQVSVQHPKTNINLIRQNIGMVFQHFHLYPHKTVLENIMLAPMKVKKVSKEEAKETAEFY 120 Query: 121 LERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 L +VG+ A +P +LSGGQQQRVAIAR LAM P VMLFDEPTSALDPEM+ EVLDVM Sbjct: 121 LNKVGIPEKADTYPSRLSGGQQQRVAIARGLAMKPEVMLFDEPTSALDPEMIGEVLDVMK 180 Query: 181 QLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQHFLEK 240 QLA EGMTM+ VTHEMGFAR+VADR++F+D+G+I+E+ F+ R RAQ FL + Sbjct: 181 QLAREGMTMVVVTHEMGFAREVADRIVFIDEGRILEESTPAAFYE--KPREKRAQLFLSR 238 Query: 241 ILQH 244 IL H Sbjct: 239 ILNH 242 Lambda K H 0.321 0.135 0.390 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: 196 Number of extensions: 5 Number of successful extensions: 2 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: 242 Length adjustment: 23 Effective length of query: 221 Effective length of database: 219 Effective search space: 48399 Effective search space used: 48399 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 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