Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease
Query= reanno::psRCH2:GFF851 (296 letters) >NCBI__GCF_000015505.1:WP_011803054.1 Length = 289 Score = 105 bits (261), Expect = 2e-27 Identities = 84/287 (29%), Positives = 136/287 (47%), Gaps = 21/287 (7%) Query: 17 HAALLAFVAAILFPLLMVISISFREGN-FATGSLF--PENPTLEHWSLALGIPYTHADGS 73 +A LL L P ++++ SF++ +G+L P + + W LA T D Sbjct: 17 YAVLLVAALFFLAPFYVMLATSFKDAEQIRSGNLLSPPASLNFDAWRLAWSSACTGVDCR 76 Query: 74 VTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPP 133 QP F WNSV +A + ++ + Y + +F G + +L L+F +F P Sbjct: 77 GLQPYF------WNSVSMAIPAVLISTAWGAVNGYVLSLWKFRG-SELLFGFLLFGVFMP 129 Query: 134 VLSLVAIYALFDQLGQHVSWLGVNSH--GAVIVASLGGMALHIWTIKGYFESIDASLEEA 191 ++ + Q + +LG++S G V+V L GMA + Y+ +I L A Sbjct: 130 FQVVLL------PMSQVLGYLGLSSSIGGLVLVHCLAGMAGTTLFFRNYYTAIPKELVNA 183 Query: 192 AIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQ 251 A +DGA W+ F+ I+LP+S PIL V I F T++ + V D ++VG Sbjct: 184 ARMDGAGFWRIFWRIVLPLSTPILMVTLIWQF-TNIWNDFLFGVAFSGADSKPITVGLNN 242 Query: 252 YLYPQNYL--WGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296 + + + AAAV++GLP V++ ++ V GLTAG VKG Sbjct: 243 MANTSSSVKSYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 289 Lambda K H 0.327 0.139 0.433 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: 261 Number of extensions: 19 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: 296 Length of database: 289 Length adjustment: 26 Effective length of query: 270 Effective length of database: 263 Effective search space: 71010 Effective search space used: 71010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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