Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 143 bits (360), Expect = 5e-39 Identities = 78/217 (35%), Positives = 125/217 (57%), Gaps = 8/217 (3%) Query: 2 ISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVD 61 I++ V KW+GD QV+ E++ GE +V GPSG GKSTL++ + LE +G +++D Sbjct: 4 ITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAMLID 63 Query: 62 GTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQLL 121 G + D P + + MVFQ + L+PH+S+ +N+ + +K G E ++K Sbjct: 64 GVDVTDH----PPAKRGLTMVFQSYALYPHMSVRENMGFS-LKTAGAPAAEIAEKVEAAA 118 Query: 122 ERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMVQ 181 + L + + P LSGGQ+QRVAI R++ P LFDEP S LD + E+ + + Sbjct: 119 AVLKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAK 178 Query: 182 LAHEGM--TMMCVTHEMGFARKVADRVIFMDQGKIIE 216 L H+ + TM+ VTH+ A +ADR++ ++ GKI + Sbjct: 179 L-HQSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQ 214 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: 188 Number of extensions: 7 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: 349 Length adjustment: 26 Effective length of query: 218 Effective length of database: 323 Effective search space: 70414 Effective search space used: 70414 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: 48 (23.1 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