Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate GFF1457 HP15_1422 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__Marino:GFF1457 Length = 240 Score = 235 bits (599), Expect = 7e-67 Identities = 125/241 (51%), Positives = 165/241 (68%), Gaps = 2/241 (0%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60 MIS++NV+K +GD +VL S +VKKGEV+ V G SGSGKSTL+ C+NA+EP KG ++V Sbjct: 1 MISVQNVHKSFGDLEVLKGVSLDVKKGEVVSVIGGSGSGKSTLLYCINAIEPINKGKILV 60 Query: 61 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQL 120 D + +TN KLR ++GMVFQ + FPH+++++N +A V SKEEA + A + Sbjct: 61 DDVDVHAKETNKDKLRQKLGMVFQQWNSFPHMTVLENAALAPRIVKKMSKEEAIEIAKKE 120 Query: 121 LERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 LE VGL +P ++SGGQQQR+AIARALAM P ML DE TSALDPE+V EVLD + Sbjct: 121 LEHVGLGDKFDVYPTKMSGGQQQRLAIARALAMKPDYMLLDEVTSALDPELVGEVLDTLR 180 Query: 181 QLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQHFLEK 240 LA EGMTM+CVTHEMGFAR V+DRV + +G I E + + D ++ Q FL K Sbjct: 181 LLAEEGMTMICVTHEMGFARDVSDRVAYFHEGVIAEIGEARQVITD--PQNPLTQKFLSK 238 Query: 241 I 241 + Sbjct: 239 V 239 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: 191 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: 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 (21.9 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