Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000012965.1:WP_011373501.1 Length = 261 Score = 112 bits (280), Expect = 1e-29 Identities = 75/239 (31%), Positives = 119/239 (49%), Gaps = 17/239 (7%) Query: 12 TYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG-----D 66 TY P+VK ++ + T +GPSGCGKTT LR + D+ N Y G D Sbjct: 21 TYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYPNNKYSGEITFKD 80 Query: 67 RRV----NDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVP-KAEIDRRVQEAAK 121 R + D+ I M+FQ +P M+++ N+A+GLKL+ + + E+ RV++A K Sbjct: 81 RNILTSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYGLKLQGIKNRTELSGRVEKALK 139 Query: 122 IL----DIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAE 177 ++ L LSGGQ+QR+ + RA+ EP+V L DEP S LD + Sbjct: 140 DAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLFDEPTSALDPISTGGIEEL 199 Query: 178 IRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFI 236 I +L +R+ ++I VTH+ +A + D M G + + + ++ PK +I Sbjct: 200 IVELRERV--SIIIVTHNMQQAARVSDYTGFMYLGELIELGKTEEIFVTPKEKLTEEYI 256 Lambda K H 0.321 0.138 0.395 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: 242 Number of extensions: 11 Number of successful extensions: 4 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: 384 Length of database: 261 Length adjustment: 27 Effective length of query: 357 Effective length of database: 234 Effective search space: 83538 Effective search space used: 83538 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: 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