Align putrescine transport system permease protein PotH (characterized)
to candidate H281DRAFT_01543 H281DRAFT_01543 putative spermidine/putrescine transport system permease protein
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__Burk376:H281DRAFT_01543 Length = 303 Score = 165 bits (417), Expect = 1e-45 Identities = 77/202 (38%), Positives = 128/202 (63%) Query: 95 YFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIRVYAW 154 Y D +L + +++ I T LL+GYP+A+ A P ++L +VILP WTS L+R YAW Sbjct: 80 YLDTFLMTFKLSVIVTGVTLLLGYPVAYFAASVSPRWSALILGMVILPFWTSVLVRTYAW 139 Query: 155 MGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRIDYSL 214 + +L+ G++N LL G++D+P+ + + + +V+ +PFMVLP+Y+A+ +I +L Sbjct: 140 LVLLQRTGLINKALLATGLVDRPVQLAYNQFGTILAMVHILLPFMVLPLYSAMQKIPANL 199 Query: 215 VEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIMIGRVL 274 +A LG PL F+ V +PL+ G++AG+ LVF+ +G ++ PEL+GG SIM+ V+ Sbjct: 200 SQAGASLGGSPLHVFWRVFLPLSMSGVVAGATLVFVLCLGFYITPELMGGGKSIMVSMVV 259 Query: 275 WQEFFNNRDWPVASAVAIIMLL 296 + W ASAV++++LL Sbjct: 260 SRNVEIYNSWGAASAVSVVLLL 281 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: 273 Number of extensions: 13 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: 317 Length of database: 303 Length adjustment: 27 Effective length of query: 290 Effective length of database: 276 Effective search space: 80040 Effective search space used: 80040 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