Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate SM_b20002 SM_b20002 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Smeli:SM_b20002 Length = 358 Score = 340 bits (871), Expect = 5e-98 Identities = 186/368 (50%), Positives = 243/368 (66%), Gaps = 20/368 (5%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 M+ + L + K+Y G +K +LDI+ EF VFVGPSGCGK+T LRMIAGLE+I+ G Sbjct: 1 MSELQLSDVRKSYGGLE--VIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +L I D R+NDV P R IAMVFQ+YALYPHMTV +NM F L+ VP+AEI++RV EAA Sbjct: 59 DLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 IL++ LLDRKPK LSGGQRQRVA+GRAIVR P++FL DEPLSNLDA+LRV MR EI + Sbjct: 119 HILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIAR 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH++L TT++YVTHDQ EAMT+ D+IVVMR GV++Q +P +Y P N+FVAGFIGSP Sbjct: 179 LHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPK 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSI-SLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 MNF++G I D D Y R P ++P + A G V +G+RPE H +E Sbjct: 239 MNFLKGVIEIDEDQAYARLPDYGDAKIP------VTLQAAAGTAVTIGIRPE--HFDEA- 289 Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYL---HTSIGPNTIVARVNPRHVYHVGSSVKLAIDLN 356 + L + ++++EH+G E + H G +V N R + G + D Sbjct: 290 ----GPAALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGL-KTGDRLTARFDPV 344 Query: 357 KIHIFDAE 364 + +FD E Sbjct: 345 SVLVFDGE 352 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: 438 Number of extensions: 16 Number of successful extensions: 3 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: 358 Length adjustment: 30 Effective length of query: 354 Effective length of database: 328 Effective search space: 116112 Effective search space used: 116112 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