Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 261 bits (668), Expect = 2e-74 Identities = 155/382 (40%), Positives = 216/382 (56%), Gaps = 43/382 (11%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V + K + G V +L + + EF V +GPSG GKTT LR+IAGLE T G Sbjct: 1 MATVETRSLTKRFDGTN--AVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 ++ +G R V +PP+ ++AMVFQ+YALYPH++V N+AF L+ +++P+ I R+V AA Sbjct: 59 DILVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 + I HLL RKP+ LSGG+RQRVAL RA+VREP FL+DEPLSNLDAKLR R E+++ Sbjct: 119 ALFGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQ 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 L +RL TT IYVTHDQ EA+ +GDR+ ++ G + Q TPQ VY QP + FVA FIGSP Sbjct: 179 LQRRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIGSPP 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300 MN + D DA +V G RPE EV+ Sbjct: 239 MNLV------DTDA-----------------------------LVTGFRPEHFLPREVYG 263 Query: 301 TTYPDSVLQMQVEVVEHMGSE--VY--LHTSIGPNTIVARVNPRHVY--HVGSSVKLAID 354 + + +E++GS+ VY L + P +++R+ + G+ A+ Sbjct: 264 SDEALEPFPFHITRIENLGSDRLVYGLLEPPLPPAKVISRIPCTVTFPLETGARYPFAVR 323 Query: 355 LNKIHIFDAETEESIGFAAGPA 376 + FD + S+G A+ A Sbjct: 324 RADLRRFDPRSGASLGVASSVA 345 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: 363 Number of extensions: 17 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: 384 Length of database: 351 Length adjustment: 30 Effective length of query: 354 Effective length of database: 321 Effective search space: 113634 Effective search space used: 113634 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