Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 210 bits (534), Expect = 6e-59 Identities = 106/271 (39%), Positives = 168/271 (61%), Gaps = 6/271 (2%) Query: 23 DFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMV 82 D NL++Q+ E+ + +GP+G GKT L IAG+ +G + +R + + P+ R + V Sbjct: 18 DINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVGFV 77 Query: 83 FQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQRQ 142 +Q+YAL+PH+TV +N+ FG ++RK+PK I ++ E +L I HLL+R P LSGG++Q Sbjct: 78 YQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGEQQ 137 Query: 143 RVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTM 202 R AL RA++ P++ L+DEPLS LD + + + E++K+HQ L+TT ++VTHD EAM + Sbjct: 138 RTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAMYL 197 Query: 203 GDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAPSI 262 D+I VM G I Q TPQ ++ +P+N FVA F+G N G++ D + AP + Sbjct: 198 ADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVG--IENIFEGQVNDDKVSL---APDV 252 Query: 263 SLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293 + + G+ G +K + + + L P DL Sbjct: 253 DIFVNTGKQGKVKVA-VPPEDIALSKEPFDL 282 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: 320 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 344 Length adjustment: 29 Effective length of query: 355 Effective length of database: 315 Effective search space: 111825 Effective search space used: 111825 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: 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