Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_090447139.1 BLS63_RS17880 maltose/maltodextrin ABC transporter ATP-binding protein MalK
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_900100495.1:WP_090447139.1 Length = 371 Score = 169 bits (428), Expect = 1e-46 Identities = 114/357 (31%), Positives = 185/357 (51%), Gaps = 13/357 (3%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 + L +I K G + L ++ G V +G + GK++L+R++AGL+ ++G + + Sbjct: 4 VTLRNICKSYGDIAITRQIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDISSGDLLIG 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLR--GEKNIDARVREIASRLHI 120 + V +P +R+V MV+Q + YP M VA N+A LKL + I +V E++ L + Sbjct: 64 EQRVNDLPPMERSVGMVFQSYALYPHMTVAENMAFGLKLAKVDKGAIRRKVEEVSRILQL 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 D L+R P +LSGGQ+QRVA+ R + + + L DEPL NLD LR ++R E+++L Sbjct: 124 DQLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAALRVQMRIEISRLHQRL 183 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL-- 238 +ST++Y T + EA+ + VL+ GQ+ Q G E++H P + VA P MN Sbjct: 184 RSTMIYVTHDQVEAMTMADKIVVLNAGQIAQVGQPLELYHYPRNQFVAGFLGSPQMNFLK 243 Query: 239 ---MAASATAQGVRLQGGAELTLPLPQGAATAAG--LTVGVRASALRVHARPGDVSVAGV 293 + AS+ A + + GG + + L G+ AG LT+GVR V A D + G Sbjct: 244 VKALGASSEAVEIEMPGGYRMQV-LVDGSEVQAGDELTLGVRPEHF-VDAEQADFAFYGQ 301 Query: 294 VELAEISGSDTFVHASTPWGD--LVAQLTGVHYFELGTAITLHLDPAQAYVFGADGR 348 + +AE G ++ S D + + G + L Q ++F ADG+ Sbjct: 302 IGVAERLGDHNLIYLSLEGVDDMITLRSDGNRKVAVSQTYAAGLMANQCHLFRADGQ 358 Lambda K H 0.318 0.133 0.375 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: 260 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: 363 Length of database: 371 Length adjustment: 30 Effective length of query: 333 Effective length of database: 341 Effective search space: 113553 Effective search space used: 113553 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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