Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 338 bits (868), Expect = 1e-97 Identities = 194/366 (53%), Positives = 247/366 (67%), Gaps = 17/366 (4%) Query: 1 MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 M V L K +GDV V D++L I DGEF VFVGPSGCGKSTLLRMIAGLE +SG++ Sbjct: 1 MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60 Query: 61 FIGETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEV 120 IG+ + + A+RGV MVFQSYALYPH++V +NM FGLK+ G KE + ++V + + + Sbjct: 61 HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120 Query: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 L+L L+RKPKALSGGQRQRVAIGR +V P VFL DEPLSNLDA LRV MR+EI+RLH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180 Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 K +G TMIYVTHDQVEAMTLADKIVVL AGRV QVG P+ELY P +RFVAGFIGSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSMN 240 Query: 241 FLPVKVTATAIEQVQVELPNRQ---QIWLPVESRGVQVGANMSLGIRPEHLLPSDIADVT 297 FL V + V L NR+ + LP + G+ + LG+RP+HL + AD + Sbjct: 241 FLEGTVQGDGV--VVPALENRRVATSVALPAD------GSKVLLGLRPQHLSVT-AADSS 291 Query: 298 LEGEVQVVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDG 357 L +++ E+LG + ++ P + +V + D L EG A+G ++F DG Sbjct: 292 LVLDLR--ERLGGVSYDYLSTPTGEKLIVETRGDEAL-PEGTAVALGFDDADAYIF--DG 346 Query: 358 SACRRL 363 + +RL Sbjct: 347 ATEQRL 352 Lambda K H 0.321 0.138 0.396 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: 359 Number of extensions: 12 Number of successful extensions: 2 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: 369 Length of database: 353 Length adjustment: 29 Effective length of query: 340 Effective length of database: 324 Effective search space: 110160 Effective search space used: 110160 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