Align putrescine transport system permease protein PotH (characterized)
to candidate 15563 b1442 predicted spermidine/putrescine transporter subunit (NCBI)
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__Keio:15563 Length = 313 Score = 132 bits (331), Expect = 1e-35 Identities = 87/282 (30%), Positives = 153/282 (54%), Gaps = 28/282 (9%) Query: 36 PYIWLILLFLLPFL---IVFKISLAEMARAIPPYTELMEWADGQLSIT--LNLGNFLQLT 90 P + L LL L P + IV+ SL + + + D +S+T L L N L Sbjct: 25 PGLGLFLLLLGPLMWFGIVYFGSLLTLL-----WQGFYTFDDFTMSVTPELTLANIRALF 79 Query: 91 DDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVA-HSKPSTRNILLLLVILPSWTSFLI 149 + P +D L++L +A T ++ +P+AW +A ++ + + V+LP W S+++ Sbjct: 80 N-PANYDIILRTLTMAVAVTIASAILAFPMAWYMARYTSGKMKAFFYIAVMLPMWASYIV 138 Query: 150 RVYAWMGILKNNGVLNNFLLWLGVIDQPL-------------TILHTNLAVYIGIVYAYV 196 + YAW +L +GV FL LG+ +PL T+ + L ++ +Y ++ Sbjct: 139 KAYAWTLLLAKDGVAQWFLQHLGL--EPLLTAFLTLPAVGGNTLSTSGLGRFLVFLYIWL 196 Query: 197 PFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEF 256 PFM+LP+ AL R+ SL++A+ DLGARP +TF V++PL GI AGS+ F +G+F Sbjct: 197 PFMILPVQAALERLPPSLLQASADLGARPRQTFRYVVLPLAIPGIAAGSIFTFSLTLGDF 256 Query: 257 VIPELLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLL 298 ++P+L+ GP IG +++ + + P+A+A ++ ++L+ Sbjct: 257 IVPQLV-GPPGYFIGNMVYSQQGAIGNMPMAAAFTLVPIILI 297 Lambda K H 0.328 0.144 0.457 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: 295 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 317 Length of database: 313 Length adjustment: 27 Effective length of query: 290 Effective length of database: 286 Effective search space: 82940 Effective search space used: 82940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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