Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__WCS417:GFF1168 Length = 344 Score = 227 bits (579), Expect = 3e-64 Identities = 123/250 (49%), Positives = 163/250 (65%), Gaps = 4/250 (1%) Query: 25 NLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMVFQ 84 ++DIQD EF +GPSG GKTT LR+IAG E + G++ I +PP RD+ VFQ Sbjct: 24 SIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIHGEEAAGLPPYQRDVNTVFQ 83 Query: 85 NYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQRQRV 144 +YAL+PHM V N+A+GLK++ V K E R +EA ++ + DRKP LSGGQRQRV Sbjct: 84 DYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVALGGYGDRKPVQLSGGQRQRV 143 Query: 145 ALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTMGD 204 AL RA+V P+V L+DEPL LD KLR QM++E++KL ++L T I+VTHDQTEA++M D Sbjct: 144 ALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQLGITFIFVTHDQTEALSMSD 203 Query: 205 RIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQ--DGDAFYFRAPSI 262 R+ V G I+Q DTP+ +Y +P FVA F+G+ N IRGE+ Q G A F Sbjct: 204 RVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGT--SNVIRGELAQRLGGTAQPFSIRPE 261 Query: 263 SLRLPEGRYG 272 +R EG G Sbjct: 262 HVRFAEGPLG 271 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: 340 Number of extensions: 13 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: 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 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