Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein
Query= TCDB::Q97Q42 (385 letters) >NCBI__GCF_000009985.1:WP_011383734.1 Length = 452 Score = 142 bits (358), Expect = 2e-38 Identities = 84/214 (39%), Positives = 128/214 (59%), Gaps = 9/214 (4%) Query: 5 IIEFKNVSKVFEDSNTK---VLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATT 61 +++ + V K F + + VL+ ++F+LEEG+ LLG SGSGKST+L I+AGL+ A Sbjct: 10 LLDLRGVRKTFLTPDRRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANG 69 Query: 62 GDIMLDGVRINDIPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQRVAEV 121 G++ G + + + VFQS+ALFP + V ENV L + K E E+R E Sbjct: 70 GEVKYRGHLMTG---PAKGISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEA 126 Query: 122 LKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELR 181 + ++ L GYE ++LSGG RQRV ARA++ +P V+LLDEP SALD+ ++ +L Sbjct: 127 IDLIGLGGYESAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLL 186 Query: 182 ELQQRLGIT---FVFVTHDQEEALAMSDWIFVMN 212 EL I + V+H+ EEA++M+D + V + Sbjct: 187 ELWDERKIPTKGILLVSHNIEEAVSMADRVLVFS 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: 393 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 385 Length of database: 452 Length adjustment: 31 Effective length of query: 354 Effective length of database: 421 Effective search space: 149034 Effective search space used: 149034 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: 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