Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Putida:PP_3817 Length = 382 Score = 227 bits (579), Expect = 4e-64 Identities = 118/286 (41%), Positives = 181/286 (63%), Gaps = 8/286 (2%) Query: 4 VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63 V+LR + K Y ++DL+I+DGEF+ F+G SG GKST L ++AG E +SG++L+D Sbjct: 15 VSLRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEILVD 74 Query: 64 NQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123 Q + ++PP R +GMVFQ Y+L+PH+ V +N+AF L + + E +RV+A+ +++QL Sbjct: 75 GQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLVQL 134 Query: 124 DKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRI 183 ++ RKP +SGGQ+QRVAI R +V EP++ L DEPL LD LR ++ E+ +LH+R+ Sbjct: 135 EQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHRRL 194 Query: 184 RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVE 243 T++YVTHDQ EAM L+ +I + + G+I +G LY P N FVA FLG+ NF+ Sbjct: 195 GITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLGN--SNFLR 252 Query: 244 VRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFV 289 ++A S + G P+ + + + D L + +RPE V Sbjct: 253 IKASSNGAGSF-----EGQPVAIRLTPGLAASQDALIM-VRPEKAV 292 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: 344 Number of extensions: 10 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: 382 Length adjustment: 30 Effective length of query: 341 Effective length of database: 352 Effective search space: 120032 Effective search space used: 120032 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 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