Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 233 bits (594), Expect = 6e-66 Identities = 122/297 (41%), Positives = 186/297 (62%), Gaps = 10/297 (3%) Query: 4 VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63 +++R I KS+DGT +++LDI GE +G SG GKSTLLR++AG E +G +++D Sbjct: 15 LSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLD 74 Query: 64 NQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123 Q V LPP R M+FQSYAL+PHMTV +N+A GLK + K EI+ RV A+ +++++ Sbjct: 75 GQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKM 134 Query: 124 DKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRI 183 + RKP+ LSGGQ+QRVA+ R++ + PK+ L DEP+ LD LR +M++E+ + + + Sbjct: 135 EPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENV 194 Query: 184 RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVE 243 +T + VTHDQ EAMT+A +I ++ G IAQ+G P+ +Y P +R A F+GS + Sbjct: 195 GATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGSVNIFEAH 254 Query: 244 VRAISASPETVTIELPSGYPLTLPV--DGSAVSPGDPLT--LGIRPEH-FVMPDEAD 295 +R A T+T +L L PV D +P + + +RPE ++ PD+ D Sbjct: 255 IREDEADSVTLTSDL-----LDAPVFIDRGVTTPAESTATLVALRPEKIYLTPDKPD 306 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: 298 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: 372 Length adjustment: 30 Effective length of query: 341 Effective length of database: 342 Effective search space: 116622 Effective search space used: 116622 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