Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= TCDB::Q97Q42 (385 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 140 bits (354), Expect = 3e-38 Identities = 92/237 (38%), Positives = 138/237 (58%), Gaps = 18/237 (7%) Query: 5 IIEFKNVSKVF--EDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTG 62 +++ ++SKV+ E T L+D N +++EG+F + G SGSGK+T L I AGLL+ TG Sbjct: 1 MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTI-AGLLETFTG 59 Query: 63 -DIMLDGVRINDIPTNKRD------VHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIE 115 + LDGV ++++ N R + +FQ++ L P +NV++NV PLR R + E + Sbjct: 60 GEYHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERK 119 Query: 116 QRVAEVLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTD 175 QR+ + L+ V L K +LSGGQ+QRVAIARA+ PR++L DEP LD ++ Sbjct: 120 QRIMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARG 179 Query: 176 MQYELRELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINH 232 + EL E R G T V VTHD E A + V+ DG++ VD+ ++P H Sbjct: 180 VM-ELLEEIHREGATIVMVTHDPELATRAQRNVHVI-DGQV------VDLAEDPRFH 228 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: 213 Number of extensions: 9 Number of successful extensions: 2 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: 238 Length adjustment: 27 Effective length of query: 358 Effective length of database: 211 Effective search space: 75538 Effective search space used: 75538 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: 48 (23.1 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