Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate BWI76_RS06035 BWI76_RS06035 ferric transporter ATP-binding subunit
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Koxy:BWI76_RS06035 Length = 348 Score = 239 bits (611), Expect = 7e-68 Identities = 135/352 (38%), Positives = 213/352 (60%), Gaps = 18/352 (5%) Query: 2 KKPIIEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATT 61 +K +E +NV+K F + V+ +IN + +G+ TLLG SG GK+TIL ++AGL + Sbjct: 3 QKNFVELRNVTKRF--GSNMVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSE 60 Query: 62 GDIMLDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEV 121 G I +DG + +RD+ VFQSYALFPHM++ +NV + L++ + + +++ RV E Sbjct: 61 GQIYIDGEDVTHRSIQQRDICMVFQSYALFPHMSLGDNVGYGLKMLGVPRGDVKARVKEA 120 Query: 122 LKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELR 181 L MV LEG+E R + ++SGGQ+QRVA+ARA+I +P+V+L DEPLS LD LR M+ ++R Sbjct: 121 LAMVDLEGFEDRYVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIR 180 Query: 182 ELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGES 241 ELQ++ IT ++VTHDQ EA A+SD + VMN G I+Q G+P ++Y +P + F+A+F+G++ Sbjct: 181 ELQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQELYRQPASRFMASFMGDA 240 Query: 242 NILPGTMIEDYLVEFNGKRFEAVDGGMKPNEPVEVVIRPEDLRITLPEEGKLQVKVDTQL 301 N+ P ED+ V+ G R E V +RPE + ++ E + + Sbjct: 241 NLFPAAFSEDF-VDIYGYRLPRPPHFAAHGEG-SVGVRPEAITLSDRGEESQRCTIRHVA 298 Query: 302 FRGVHYEIIAYDELGNEW-------MIHSTR-KAIVGEEIGLDFEPEDIHIM 345 + G YE+ EW +++TR + VGE L+ P + ++ Sbjct: 299 YMGPQYEVTV------EWHGQEILLQVNATRLQPDVGEHYYLEIHPYGMFVL 344 Lambda K H 0.318 0.138 0.386 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: 284 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: 385 Length of database: 348 Length adjustment: 30 Effective length of query: 355 Effective length of database: 318 Effective search space: 112890 Effective search space used: 112890 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 (21.7 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