Align putrescine transport system permease protein PotH (characterized)
to candidate BWI76_RS13415 BWI76_RS13415 spermidine/putrescine ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__Koxy:BWI76_RS13415 Length = 309 Score = 133 bits (334), Expect = 6e-36 Identities = 85/277 (30%), Positives = 151/277 (54%), Gaps = 18/277 (6%) Query: 36 PYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSIT--LNLGNFLQLTDDP 93 P + L LL L P + + L + + + + D +S+T L L N L+ +P Sbjct: 21 PSLALFLLLLGPLMWFGIVYLGSLLTLL--WQSFYTFDDFTMSVTQDLTLAN-LRALFNP 77 Query: 94 LYFDAYLQSLQVAAISTFCCLLIGYPLAWAVA-HSKPSTRNILLLLVILPSWTSFLIRVY 152 +D L++L +A T ++ P+AW +A +++ + + V+LP W S++++ Y Sbjct: 78 ANYDIILRTLMMALSVTIASAILALPMAWYMARYTRGKMKAFFYIAVMLPMWASYIVKAY 137 Query: 153 AWMGILKNNGVLNNFLLWLG-------VIDQPL----TILHTNLAVYIGIVYAYVPFMVL 201 AW +L +GV FL LG V+ P T+ + L ++ VY ++PFM+L Sbjct: 138 AWTLLLAKDGVAQWFLRHLGLESLLSLVLTIPAVGGNTLSTSGLGRFLVFVYIWLPFMIL 197 Query: 202 PIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPEL 261 P+ AL R+ SL++A+ DLGARP +TF V++PL GI AGS+ F +G+F++P+L Sbjct: 198 PVQAALERLPPSLLQASADLGARPRQTFRYVVLPLAIPGIAAGSIFTFSLTLGDFIVPQL 257 Query: 262 LGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLL 298 + GP IG +++ + + P+A+A ++ ++L+ Sbjct: 258 V-GPPGFFIGNMVYSQQGAIGNMPMAAAFTLVPIVLI 293 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: 288 Number of extensions: 16 Number of successful extensions: 3 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: 309 Length adjustment: 27 Effective length of query: 290 Effective length of database: 282 Effective search space: 81780 Effective search space used: 81780 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