Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 15562 b1441 predicted spermidine/putrescine transporter subunit (NCBI)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Keio:15562 Length = 337 Score = 216 bits (549), Expect = 1e-60 Identities = 115/262 (43%), Positives = 169/262 (64%), Gaps = 6/262 (2%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 V ++ I+D EF +GPSG GKTT LR+IAG E ++ G + I + +++PP +RD+ Sbjct: 20 VDGVSIAIKDGEFFSMLGPSGSGKTTCLRLIAGFEQLSGGAISIFGKPASNLPPWERDVN 79 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 VFQ+YAL+PHM++ N+A+GL ++ V K + QEA + + + + RKP LSGGQ Sbjct: 80 TVFQDYALFPHMSILDNVAYGLMVKGVNKKQRHAMAQEALEKVALGFVHQRKPSQLSGGQ 139 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 RQRVA+ RA+V EP+V L+DEPL LD KLR QM+ E++KL Q L T I+VTHDQ EA+ Sbjct: 140 RQRVAIARALVNEPRVLLLDEPLGALDLKLREQMQLELKKLQQSLGITFIFVTHDQGEAL 199 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAM--NFIRGEIVQDGDAFYFR 258 +M DR+ V +G I+Q D+P+ +Y +P+ FVAGF+G+ + + ++ +F R Sbjct: 200 SMSDRVAVFNNGRIEQVDSPRDLYMRPRTPFVAGFVGTSNVFDGLMAEKLCGMTGSFALR 259 Query: 259 APSISLRLPEGRYGVLKASGAI 280 I L P G L+A+G I Sbjct: 260 PEHIRLNTP----GELQANGTI 277 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: 306 Number of extensions: 12 Number of successful extensions: 1 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: 337 Length adjustment: 29 Effective length of query: 355 Effective length of database: 308 Effective search space: 109340 Effective search space used: 109340 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 Sep 17 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