Align ABC transporter for Lactose, ATPase component (characterized)
to candidate PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Putida:PP_3817 Length = 382 Score = 219 bits (558), Expect = 9e-62 Identities = 120/281 (42%), Positives = 170/281 (60%), Gaps = 6/281 (2%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 + L + K YG + +DL+I+ GEF+ F+G SG GKST L M+AG E SSG++ +D Sbjct: 15 VSLRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEILVD 74 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123 + +V P KR I MVFQ Y+L+PH+ VR+N+ F L + AE KRV+ +++L Sbjct: 75 GQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLVQL 134 Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183 RKP Q+SGGQ+QRVAI RA+V P+I L DEPL LD +LR ++ E+ +LH++L Sbjct: 135 EQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHRRL 194 Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243 TIVYVTHDQ EAM L+ +I + G + +G+ DLY +P N FVA F+G+ NFL+ Sbjct: 195 GITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLGN--SNFLR 252 Query: 244 GVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPE 284 + ++ P I +T AA I +RPE Sbjct: 253 IKASSNGAGSFEGQP----VAIRLTPGLAASQDALIMVRPE 289 Lambda K H 0.321 0.139 0.396 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: 328 Number of extensions: 9 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: 358 Length of database: 382 Length adjustment: 30 Effective length of query: 328 Effective length of database: 352 Effective search space: 115456 Effective search space used: 115456 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 (21.8 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