Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 226 bits (576), Expect = 8e-64 Identities = 129/328 (39%), Positives = 191/328 (58%), Gaps = 21/328 (6%) Query: 4 VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63 V + + K +D + L I GE +G SG GKSTLLR++AG E + G +L+D Sbjct: 21 VKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLD 80 Query: 64 NQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123 Q + LPP R + M+FQSYAL+PHMTV +N+AFGLK + EI RV + +++ + Sbjct: 81 GQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLVHM 140 Query: 124 DKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRI 183 K +RKP LSGGQRQRVA+ R++ + PK+ L DEP+ LD LR QM++E+ + +R+ Sbjct: 141 AKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERV 200 Query: 184 RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVE 243 T I VTHDQ EAMT+A +I +++ G I QVG P+ +Y P NR VA F+GS +N E Sbjct: 201 GVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGS--VNIFE 258 Query: 244 VRAISASPETVTIELPS-------GYPLTLPV-DGSAVSPGDPLTLGIRPEH-FVMPDEA 294 ++ + V IE P G+ +T D SA+ +RPE FV ++ Sbjct: 259 GEIVADMDDHVIIECPQLDRQIYLGHGVTTRAEDKSAI-------YALRPEKVFVTTEQP 311 Query: 295 DFTF---HGQITVAERLGQYNLLYLTLE 319 + + HG++ LG +++ Y+ L+ Sbjct: 312 EQPYNWAHGEVHDIAYLGGHSVYYIKLD 339 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: 332 Number of extensions: 13 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: 378 Length adjustment: 30 Effective length of query: 341 Effective length of database: 348 Effective search space: 118668 Effective search space used: 118668 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 Sep 24 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