Align putrescine transport system permease protein PotH (characterized)
to candidate SM_b20283 SM_b20283 spermidine/putrescine ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__Smeli:SM_b20283 Length = 327 Score = 162 bits (410), Expect = 1e-44 Identities = 97/278 (34%), Positives = 161/278 (57%), Gaps = 15/278 (5%) Query: 31 LVIALPYIWLILLFLLPFLIVFKIS-LAEMARAIPPYTELMEWADGQLSITLNLGNFLQL 89 L+ +P W+ L + P + +IS +A+ +A DG TL N+ Sbjct: 50 LLAGVPLFWIAALHIGPIFQMGRISFMADYPQA----------PDGGSPYTL--ANYELF 97 Query: 90 TDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHS-KPSTRNILLLLVILPSWTSFL 148 D LYF +++SL AA+ T L+I YP+A+ VA +P R LLL+++P W L Sbjct: 98 FSDQLYFMPFIRSLIFAAVVTISTLVIVYPVAYYVAKIVQPKNRMRALLLLLIPFWAGEL 157 Query: 149 IRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALI 208 IR ++ + +L N G +N L LG ID+P+ +L+T+ ++ G++Y +M+LP+Y+A+ Sbjct: 158 IRTFSVIMLLANRGAVNVALRELGFIDRPIPMLYTSFSLSFGVIYLLALYMLLPLYSAIE 217 Query: 209 RIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSI 268 +I L+ AA DLGA P + F VI+PL+K GI++G LV++ +VG F P LLGGP+++ Sbjct: 218 KIPTPLIHAAADLGAGPFQRFRRVILPLSKDGIVSGCSLVYLTSVGVFAAPLLLGGPNTV 277 Query: 269 MIGRVLWQEFFNNRD-WPVASAVAIIMLLLLIVPIMWF 305 + V+ F ++ D WP +A A+++L + + + F Sbjct: 278 IFPEVIATLFHSSNDKWPEGAAFAMLLLAVSLSTVGLF 315 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: 246 Number of extensions: 20 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: 317 Length of database: 327 Length adjustment: 28 Effective length of query: 289 Effective length of database: 299 Effective search space: 86411 Effective search space used: 86411 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