Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889 Length = 386 Score = 288 bits (738), Expect = 1e-82 Identities = 163/370 (44%), Positives = 232/370 (62%), Gaps = 28/370 (7%) Query: 1 MASVQLQNVTKAWGEVVVS--KDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58 MA+++L+NV K +G + K+I L I +GEF++ VGPSGCGKSTL+ IAGLETIT G Sbjct: 1 MATLELRNVNKTYGVGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 DLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVA 118 + IG++ ++ P +R + MVFQSYALYP +SV EN+ FGLK+ + I++ V +VA Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQAAIDEEVTRVA 120 Query: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178 ++LQ+ HLL+RKP LSGGQ+QRVA+GR L P ++L DEPLSNLDA LRV+MR E+ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238 +H+RL T +YVTHDQ+EAMTL DK+ V+ G + Q G P ++Y PA+ FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240 Query: 239 MNFLPVKV------TATAID--QVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL 290 MNF+P+++ +D Q + ELPM + +E R+V LG+RPE + Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQD---AGLEDREV------ILGMRPEQI 291 Query: 291 L-----PSDIADVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAI 345 + P+ + + EVQV E G +T + + + + + R V + G T + Sbjct: 292 MLAGSEPNGLPTI--RAEVQVTEPTGPDTLVFVNLNDTK--VCCRLAPDVAPQPGETLTL 347 Query: 346 GLPPERCHLF 355 P + LF Sbjct: 348 QFDPSKVLLF 357 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: 384 Number of extensions: 12 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: 371 Length of database: 386 Length adjustment: 30 Effective length of query: 341 Effective length of database: 356 Effective search space: 121396 Effective search space used: 121396 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