Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__Smeli:SM_b20972 Length = 391 Score = 358 bits (920), Expect = e-103 Identities = 191/376 (50%), Positives = 256/376 (68%), Gaps = 16/376 (4%) Query: 1 MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 MA++++ N+ K++G + + I+L+I +GEFV F+GPSGCGKSTLLR IAGLE + G + Sbjct: 1 MATIRIDNLRKSFGSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENLDGGSI 60 Query: 61 FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120 +G++ + D P A R + MVFQ+YALYPH++V +N+SFGL L G K+ I++RVN AE+ Sbjct: 61 RLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALNGMKRNEIDRRVNNAAEI 120 Query: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180 L++ LLDRKP+ LSGGQRQRVAIGR +V EP +FLLDEPLSNLDA LRV MR+E++ LH Sbjct: 121 LRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRVELAALH 180 Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 +RLG TMIYVTHDQVEAMTL+D++VVLD GRV+Q G PLEL++ PA+ FVAGFIGSP+MN Sbjct: 181 ERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFIGSPRMN 240 Query: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVIL 300 FLP V A +V + +R S + ++LGIRP+ L + + L Sbjct: 241 FLPAGVAEQAATRVTLAGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLELTSPEEAHL 300 Query: 301 EGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGA-------TFAIGLPPERCH 353 G V++VE+LG E+ +HI++ D+ V G + LPPE CH Sbjct: 301 AGTVRLVERLGTESHVHIRVEG--------GGDLTAVVRGTHPVASRDQVHLRLPPEHCH 352 Query: 354 LFREDGTA-CRRLHKE 368 LF +GTA RRL E Sbjct: 353 LFDAEGTAIARRLDPE 368 Lambda K H 0.320 0.137 0.393 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: 401 Number of extensions: 12 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: 371 Length of database: 391 Length adjustment: 30 Effective length of query: 341 Effective length of database: 361 Effective search space: 123101 Effective search space used: 123101 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 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