Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >NCBI__GCF_000012965.1:WP_011373501.1 Length = 261 Score = 122 bits (306), Expect = 7e-33 Identities = 86/235 (36%), Positives = 131/235 (55%), Gaps = 15/235 (6%) Query: 2 ISIKNVNKWYG--DFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQ----- 54 + +KN Y D + S V K + + GPSG GK+TL++ N + Sbjct: 13 LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYPNNKY 72 Query: 55 KGDVIVDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLG-RSKEEA 113 G++ +I K +L KLR ++GM+FQ FP +SI DN+ +K+ G +++ E Sbjct: 73 SGEITFKDRNILTSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYG-LKLQGIKNRTEL 130 Query: 114 SKKALQLLERVGLSAHAK---KHPGQ-LSGGQQQRVAIARALAMDPIVMLFDEPTSALDP 169 S + + L+ + K KH LSGGQQQR+ IARA+A++P V+LFDEPTSALDP Sbjct: 131 SGRVEKALKDAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLFDEPTSALDP 190 Query: 170 EMVNEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFF 224 + +++V+L E ++++ VTH M A +V+D FM G++IE K EE F Sbjct: 191 ISTGGIEELIVEL-RERVSIIIVTHNMQQAARVSDYTGFMYLGELIELGKTEEIF 244 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: 161 Number of extensions: 12 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: 261 Length adjustment: 24 Effective length of query: 220 Effective length of database: 237 Effective search space: 52140 Effective search space used: 52140 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 Apr 09 2024. 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