Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 218 bits (555), Expect = 2e-61 Identities = 115/244 (47%), Positives = 159/244 (65%), Gaps = 2/244 (0%) Query: 4 IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63 ++ I K+F + L+ IDL + GE L +GPSGCGK+TLLR +AGLE+ SG+I Sbjct: 20 LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79 Query: 64 GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQI 123 G+ I+ + RD +VFQSYAL+P++T+AEN+ +GL + AEI RV E+ + + Sbjct: 80 GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGL 139 Query: 124 KHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNS 183 + P +LSGGQ+QRVAL RAL+ ++L DEPLS LDA +R ++R EI+RL Sbjct: 140 PTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQV 199 Query: 184 KSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLE 243 T I VTHDQ EA ++ DRI V+ GVIEQ+GTP EIY RP + F+A F+G ++N L Sbjct: 200 GITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVLR 257 Query: 244 GAVL 247 G L Sbjct: 258 GQAL 261 Lambda K H 0.318 0.136 0.383 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: 294 Number of extensions: 10 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: 347 Length of database: 377 Length adjustment: 29 Effective length of query: 318 Effective length of database: 348 Effective search space: 110664 Effective search space used: 110664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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