Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 237 bits (605), Expect = 3e-67 Identities = 133/288 (46%), Positives = 183/288 (63%), Gaps = 8/288 (2%) Query: 6 LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65 L +I K + Q + DFNL IQD EF +GPSGCGKTT LR+IAG E EG + + Sbjct: 9 LSNISKRFASQE--VLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66 Query: 66 DRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI 125 + +P + R VFQ+YAL+PH+TV+ N+AFGLK+ V +I RV +A I+ + Sbjct: 67 GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126 Query: 126 AHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRL 185 + RKP LSGGQ+QRVA+ RA+V P++ L+DE LS LD KLR QM+ E+++L ++L Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186 Query: 186 QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIR 245 T +YVTHDQ EA++M DRI+VM +G QQ TP+ +Y P+N+FVA FIG +N Sbjct: 187 GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE--INVFD 244 Query: 246 GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293 GEIVQ + + A SI+ + E R A+G V + +RPEDL Sbjct: 245 GEIVQALGEYQYEA-SINGVVREIR---CDHRFAVGDKVHVMLRPEDL 288 Score = 24.3 bits (51), Expect = 0.006 Identities = 9/32 (28%), Positives = 20/32 (62%) Query: 339 PRHVYHVGSSVKLAIDLNKIHIFDAETEESIG 370 PR +Y ++ +A + +I++FD E +++G Sbjct: 221 PREIYESPRNLFVAQFIGEINVFDGEIVQALG 252 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: 338 Number of extensions: 16 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: 2 Length of query: 384 Length of database: 369 Length adjustment: 30 Effective length of query: 354 Effective length of database: 339 Effective search space: 120006 Effective search space used: 120006 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: 50 (23.9 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