Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= TCDB::Q97Q42 (385 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 151 bits (381), Expect = 2e-41 Identities = 85/216 (39%), Positives = 130/216 (60%), Gaps = 5/216 (2%) Query: 5 IIEFKNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDI 64 II+ KN+ K +ED + L +++ E+E G+ +++G SGSGKST+LN+I GL A G I Sbjct: 6 IIKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQI 65 Query: 65 MLDGVRINDIPT----NKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAE 120 + GV + D ++ VFQ + L P++ V ENV PL ID K++E+R + Sbjct: 66 SVAGVNLMDNSDLSNFRSNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERALK 125 Query: 121 VLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYEL 180 +LK V LE + KLSGG+RQRVAIARA++N P ++L DEP ALD + + + L Sbjct: 126 LLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLL 185 Query: 181 RELQQRLGITFVFVTHDQEEALAMSDWIFVMNDGEI 216 ++ ++ +T + VTH+ A I+V+ DG+I Sbjct: 186 LDIHKKENVTLIMVTHEPYVAKQADRSIYVL-DGKI 220 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: 235 Number of extensions: 16 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: 223 Length adjustment: 26 Effective length of query: 359 Effective length of database: 197 Effective search space: 70723 Effective search space used: 70723 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 Apr 09 2024. 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