Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Putida:PP_3817 Length = 382 Score = 231 bits (589), Expect = 3e-65 Identities = 122/244 (50%), Positives = 162/244 (66%), Gaps = 4/244 (1%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 + LR +NK YG + N++L+I DGEFL +G SG GKST ++ +AG ET S G IL Sbjct: 15 VSLRGLNKHYGDFT--AVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEIL 72 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 VD + + P RDI MVFQ Y+L+P ++VRDNIAF L IRK+ AE + V + KL+ Sbjct: 73 VDGQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLV 132 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 Q+E RKP Q+SGGQQQRVA+ RAL P+I L DEPL LD KLR +++ E++ +H+ Sbjct: 133 QLEQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHR 192 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 RL T VYVTHDQ EAM L ++A+ G I GT D+Y NP N FVASF+G+ NF Sbjct: 193 RLGITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLGN--SNF 250 Query: 244 IPLR 247 + ++ Sbjct: 251 LRIK 254 Lambda K H 0.319 0.138 0.393 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: 320 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: 386 Length of database: 382 Length adjustment: 30 Effective length of query: 356 Effective length of database: 352 Effective search space: 125312 Effective search space used: 125312 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 (21.7 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