Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 234 bits (596), Expect = 4e-66 Identities = 126/282 (44%), Positives = 175/282 (62%), Gaps = 4/282 (1%) Query: 25 LTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLS 84 L + + AVD VSL + G F++LG SGCGK+TLLR+LAGF++P G I + G ++ Sbjct: 10 LVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMN 69 Query: 85 QVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAK 144 VPP RP+NM+FQ ALFP MTV NIA+GLK+ K+P E R+ +L V + + Sbjct: 70 DVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEH 129 Query: 145 RKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCV 204 R P +LSGGQRQRVALAR L P LLLLDEP+GALD KLR++M++E+ + ++ G T V Sbjct: 130 RNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFV 189 Query: 205 MVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEGVLKERQ 264 +THDQ EAM M+ ++A+M G+F Q+ PEE+Y P T + A F+G N G L + Sbjct: 190 YITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGDNNRLSGELVSVR 249 Query: 265 ED--GLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIML 304 + L LD LV + +++ RPE ++L Sbjct: 250 DSLAELRLDDGVLVQGRVASDNLQAGHRAELYI--RPESLVL 289 Lambda K H 0.321 0.137 0.400 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: 368 Number of extensions: 17 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: 377 Length of database: 362 Length adjustment: 30 Effective length of query: 347 Effective length of database: 332 Effective search space: 115204 Effective search space used: 115204 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