Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_000012965.1:WP_011373501.1 Length = 261 Score = 119 bits (297), Expect = 8e-32 Identities = 86/259 (33%), Positives = 134/259 (51%), Gaps = 29/259 (11%) Query: 16 LEIRDLHKQYGPLEV--LKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIL 73 LE+++ Y +V +K + + + + N+ LIG SG GKTTLLR N + + + Sbjct: 13 LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHD-----LY 67 Query: 74 LDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLL------ 127 + + G + + S++ + + R GM FQ+ FP ++ NV GL Sbjct: 68 PNNKYSGEITFKDRNILTSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYGLKLQGIKN 126 Query: 128 ------KVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSL 181 +V+K KD A+ W E + +R H LSGGQQQR+ IARA+A+ P + Sbjct: 127 RTELSGRVEKALKDAAI-----WNE---VKDRLKHDANGLSGGQQQRLCIARAVAVEPEV 178 Query: 182 MLFDEVTSALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQ 241 +LFDE TSALDP G + +I L E +++++VTH M+ A VSD FM G + E Sbjct: 179 LLFDEPTSALDPISTGGIEELIVELRE-RVSIIIVTHNMQQAARVSDYTGFMYLGELIEL 237 Query: 242 GPPKELFERPQSPRLAEFL 260 G +E+F P+ E++ Sbjct: 238 GKTEEIFVTPKEKLTEEYI 256 Lambda K H 0.319 0.135 0.379 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: 132 Number of extensions: 10 Number of successful extensions: 3 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: 265 Length of database: 261 Length adjustment: 25 Effective length of query: 240 Effective length of database: 236 Effective search space: 56640 Effective search space used: 56640 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 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