Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 260 bits (665), Expect = 3e-74 Identities = 142/322 (44%), Positives = 193/322 (59%), Gaps = 39/322 (12%) Query: 1 MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 MA+V+ +++TK + I+L +HE EF+V +GPSG GK+TLLR+IAGLE TSGD+ Sbjct: 1 MATVETRSLTKRFDGTNAVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSGDI 60 Query: 61 FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120 +G + + PP + MVFQSYALYPHLSVA N++F L+ +E I ++V+ A + Sbjct: 61 LVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAAAL 120 Query: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180 + HLL RKP+ LSGG+RQRVA+ R +V EP FLLDEPLSNLDA LR R E+ +L Sbjct: 121 FGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQLQ 180 Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 +RL T IYVTHDQ+EA+ L D++ +LD GRV Q+G P ++Y PAD FVA FIGSP MN Sbjct: 181 RRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIGSPPMN 240 Query: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDI--ADV 298 + T G RPEH LP ++ +D Sbjct: 241 LVDTDALVT----------------------------------GFRPEHFLPREVYGSDE 266 Query: 299 ILEG---EVQVVEQLGNETQIH 317 LE + +E LG++ ++ Sbjct: 267 ALEPFPFHITRIENLGSDRLVY 288 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: 317 Number of extensions: 9 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: 371 Length of database: 351 Length adjustment: 29 Effective length of query: 342 Effective length of database: 322 Effective search space: 110124 Effective search space used: 110124 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