Align putrescine transport system permease protein PotH (characterized)
to candidate WP_004307352.1 C665_RS09740 binding-protein-dependent transporter system inner membrane protein
Query= CharProtDB::CH_088338 (317 letters) >NCBI__GCF_000310185.1:WP_004307352.1 Length = 314 Score = 279 bits (713), Expect = 7e-80 Identities = 138/296 (46%), Positives = 201/296 (67%), Gaps = 14/296 (4%) Query: 27 HGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWA--DGQLSITLNLG 84 HGR V LP++W++ F+LPF ++ +SL+ A+PPY A DG + + Sbjct: 11 HGRFWVGLLPWVWMLFFFVLPFALIVNVSLSTPDLAVPPYVSPFAGAAVDGAPAFRPDPA 70 Query: 85 NFLQL----------TDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNI 134 ++ +L D Y AY SL +AA++T CCL++GYP A+ +A + + RN+ Sbjct: 71 SYARLGGELAALGTLAADRPYLAAYANSLLLAALTTLCCLVLGYPFAYRLARAPEAMRNL 130 Query: 135 LLLLVILPSWTSFLIRVYAWMGILKNN--GVLNNFLLWLGVIDQPLTILHTNLAVYIGIV 192 LL+LV+LP WTSFL+RVYAWMG+L ++ G++N LL LG++ +PL +L+ AV +G+V Sbjct: 131 LLMLVMLPFWTSFLLRVYAWMGLLDSSETGLINQVLLGLGLVAEPLPLLYNTGAVLVGMV 190 Query: 193 YAYVPFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPA 252 Y+Y+PFMVLP+Y L+++D L EAA DLGARP F + +PL+ GI+AGSMLVFIPA Sbjct: 191 YSYLPFMVLPLYANLVKLDQRLPEAARDLGARPATVFLRITLPLSSRGIVAGSMLVFIPA 250 Query: 253 VGEFVIPELLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKH 308 VGEFVIP+LLGG + IGR +W +F N+DWP+A+AVA++M+ +LI PI+ +H Sbjct: 251 VGEFVIPDLLGGGSVMTIGRSIWDDFGPNQDWPMAAAVAVLMVAMLIAPIVLLQRH 306 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: 312 Number of extensions: 15 Number of successful extensions: 4 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: 314 Length adjustment: 27 Effective length of query: 290 Effective length of database: 287 Effective search space: 83230 Effective search space used: 83230 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 24 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