Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 216 bits (550), Expect = 8e-61 Identities = 127/325 (39%), Positives = 188/325 (57%), Gaps = 8/325 (2%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 L + G+ K++ + N+NLDI +GE+ +G SG GKSTLLRM+AG E G++ +D Sbjct: 15 LSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLD 74 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123 G V +PP R M+FQSYAL+PHMTV +N++ LK K ++EI V A + +++ Sbjct: 75 GQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKM 134 Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183 Y R P+ LSGGQ+QRVA+ RS+ + PK+ L DEP+ LD LR +LE+ ++ E + Sbjct: 135 EPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENV 194 Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243 +T + VTHDQ EAMT+A+RI ++A G IAQ+GSP+++YE P + A+FIGS +N+ Sbjct: 195 -GATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGS--VNIF 251 Query: 244 PGKIIGTGAQTTVEMTD--GGRAVSDYPSDDSLMGAAVNVGVRPED--MVEAAPGGDYVF 299 I A + +D D A V +RPE + P G+ + Sbjct: 252 EAHIREDEADSVTLTSDLLDAPVFIDRGVTTPAESTATLVALRPEKIYLTPDKPDGENNW 311 Query: 300 E-GKVAITEALGEVTLLYFEAPSGE 323 G V LG++T Y + SG+ Sbjct: 312 SCGTVDNIAYLGDITSYYVKLASGK 336 Lambda K H 0.316 0.135 0.379 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: 338 Number of extensions: 14 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: 373 Length of database: 372 Length adjustment: 30 Effective length of query: 343 Effective length of database: 342 Effective search space: 117306 Effective search space used: 117306 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 (21.6 bits) S2: 50 (23.9 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