Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 377 bits (968), Expect = e-109 Identities = 210/359 (58%), Positives = 249/359 (69%), Gaps = 5/359 (1%) Query: 6 LRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQ 65 L ++ K G I R + L+I GEFVVFVGPSGCGKSTLLRLIAGL+ I GDLLID + Sbjct: 6 LDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGR 65 Query: 66 RVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDK 125 RVNDL P++R VGMVFQSYALYPHM+V +N++FGLKLA DK ++ RV A+ILQLDK Sbjct: 66 RVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDK 125 Query: 126 LLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRS 185 LL+RKPK+LSGGQRQRVA+GR M REP + LFDEPLSNLDA LRVQMR EIARLH R+ S Sbjct: 126 LLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGS 185 Query: 186 TMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVR 245 TMIYVTHDQVEAMTLADKIVVLN G + QVG P LY P +RFVAGFLGSP+MNF+ R Sbjct: 186 TMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSAR 245 Query: 246 AISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHGQITVA 305 + ET ++ +LP D S ++ G PL+LGIRPEH V AD T +T Sbjct: 246 -LQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEH-VSLKAADGTAGVVVTAV 303 Query: 306 ERLGQYNLLYLTLERLQDVITLC-VDGNLRVTEGETFAAGLKADKCHLFRENGEACTRH 363 E LG Y+ LE QD +C + + G+ L D HLF +G A +RH Sbjct: 304 EYLGSET--YVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALSRH 360 Lambda K H 0.322 0.139 0.405 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: 433 Number of extensions: 18 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: 381 Length adjustment: 30 Effective length of query: 341 Effective length of database: 351 Effective search space: 119691 Effective search space used: 119691 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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