Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 221 bits (562), Expect = 3e-62 Identities = 121/281 (43%), Positives = 168/281 (59%), Gaps = 6/281 (2%) Query: 6 LRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQ 65 L + K + +DL I G F +G SGCGK+T LR+I+GLE T+G + + +Q Sbjct: 21 LTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLGDQ 80 Query: 66 RVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDK 125 V D P R V VFQ+YAL+PH+ + EN+AFGL+ + R +K+ VE + ++++L Sbjct: 81 DVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGI--RSVKKPVEDMLDLVELGH 138 Query: 126 LLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRS 185 L RKP LSGGQ+QR+A+ R ++ +P+V L DEPL LD LR QM+IE+ R+ + Sbjct: 139 LARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGL 198 Query: 186 TMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVR 245 T ++VTHDQ EAMT+AD I V+N G I Q+G P LY P FVA FLG Q N + Sbjct: 199 TFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNLIAGT 256 Query: 246 AISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPE 286 S S + V + G L LP + G P+ LG+RPE Sbjct: 257 VESVSGDVVQV-AAHGRSLALPAARCRTTSG-PVILGVRPE 295 Lambda K H 0.322 0.139 0.405 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: 329 Number of extensions: 16 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: 371 Length of database: 386 Length adjustment: 30 Effective length of query: 341 Effective length of database: 356 Effective search space: 121396 Effective search space used: 121396 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: 50 (23.9 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