Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Marino:GFF2209 Length = 366 Score = 225 bits (573), Expect = 2e-63 Identities = 134/364 (36%), Positives = 204/364 (56%), Gaps = 30/364 (8%) Query: 1 MASVTLRDICKSYDGTPI------TRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLED 54 MA + L+ + SY P R +D G +GPSGCGKST+L +I+GL Sbjct: 1 MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ 60 Query: 55 ITSGDLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRV 114 + GD+L D +RVN+L P+DR++ VFQ +Y MTV +N+AF LK V +IK RV Sbjct: 61 PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV 120 Query: 115 EAVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREP-KVFLFDEPLSNLDAFLRVQMR 173 +AE+L+++ L +K K+L+ ++Q+V++GR +VRE LFDEPL+ +D L+ ++R Sbjct: 121 HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR 180 Query: 174 IEIARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGF 233 ++ ++H++ TM+YVTHDQ+EA T ADKI V+ G+I Q G P L+ P + FV F Sbjct: 181 RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF 240 Query: 234 LGSPQMNFVEV----RAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFV 289 +GSP MN +EV R + V++E + VD + + +GIRPE Sbjct: 241 IGSPGMNLIEVQRCPRGVCFGSTVVSLE-------SWQVDVLQRTRSTNIKIGIRPEFVE 293 Query: 290 MPDEA-DFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKAD 348 + A D TF ++ E LG Y ++ + L+ ++V + E FAA + Sbjct: 294 VSSVASDDTFEAEVLDVEDLGTYKIVTVQLDH----------EKMKVRQSEEFAASI-GS 342 Query: 349 KCHL 352 K HL Sbjct: 343 KVHL 346 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: 305 Number of extensions: 13 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: 366 Length adjustment: 30 Effective length of query: 341 Effective length of database: 336 Effective search space: 114576 Effective search space used: 114576 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: 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