Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate WP_110753066.1 C7477_RS13715 carbohydrate ABC transporter permease
Query= BRENDA::P68183 (296 letters) >NCBI__GCF_003217235.1:WP_110753066.1 Length = 274 Score = 127 bits (318), Expect = 4e-34 Identities = 87/285 (30%), Positives = 146/285 (51%), Gaps = 27/285 (9%) Query: 16 THLLLLLFIAAIMFPLLMVVAISLRQGNFATGS----LIPEQISWDHWKLALGFSVEQAD 71 T LL+ + ++ +F + ++++SL+ G+ LIPE+ +W ++ + Sbjct: 12 TALLVFVIVSPAIFFFVWMLSLSLKY-EIDNGAYPPILIPERFAWSNYTQIFAEN----- 65 Query: 72 GRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMF 131 LL+ WNS+ V G++ + + + Y AR++ A ++ +I +M Sbjct: 66 --------DFLLYFWNSLLVTGMATLLALLVGVPAGYGIARLKAHKSAVVI---MIARMT 114 Query: 132 PAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEA 191 P + L+ L+ LF LG +G +I + + + +W + GYFE LEEA Sbjct: 115 PGLSYLIPLFLLFQTLG----LLG-TLWPQIIIHLVVTVPIVIWIMIGYFEATPMELEEA 169 Query: 192 AALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQ 251 A +DGA WQ FRLV LP++ P + V IL+ I + V ++L + TL V + Sbjct: 170 AQIDGANAWQVFRLVALPIAKPGIVVSLILAVIFSWNNF-VFGIVLASRETRTLPVAVYN 228 Query: 252 YLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296 L+ + WG AAAA++ LP+ ++ +LAQR +V GLTAG VKG Sbjct: 229 MLSFEQVSWGPLAAAALVVTLPVLLLTVLAQRQIVAGLTAGAVKG 273 Lambda K H 0.328 0.141 0.435 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: 259 Number of extensions: 20 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: 274 Length adjustment: 26 Effective length of query: 270 Effective length of database: 248 Effective search space: 66960 Effective search space used: 66960 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. 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