Align putrescine transport system permease protein PotH (characterized)
to candidate Pf6N2E2_4516 Putrescine transport system permease protein PotH (TC 3.A.1.11.2)
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4516 Length = 306 Score = 372 bits (954), Expect = e-108 Identities = 173/286 (60%), Positives = 231/286 (80%) Query: 28 GRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFL 87 GR+LVI +P+IWL L F+LPF IV KIS AE AIPPYTE+ + D +L + LNL N+ Sbjct: 17 GRQLVIGVPFIWLFLFFMLPFFIVLKISFAEADVAIPPYTEIYSYVDQKLQVLLNLANYA 76 Query: 88 QLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSF 147 L++D LY AYL SL++A IST CLLIGYP+A+ +A+++ + +L+LL+++P+WT+ Sbjct: 77 MLSEDELYIAAYLGSLKMALISTVLCLLIGYPMAYGIANARKEMQTVLVLLIMMPTWTAI 136 Query: 148 LIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTAL 207 LIRVYAWMGIL NNG+LN FLL +G I++PL IL+TNLAVYIG+VY+Y+PFM+LP+Y L Sbjct: 137 LIRVYAWMGILSNNGLLNGFLLSMGFINEPLQILNTNLAVYIGVVYSYLPFMILPLYANL 196 Query: 208 IRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDS 267 ++ D SL+EAA DLG+ +F+ + VPL+K GI+AG MLVFIP VGEFVIPELLGGP++ Sbjct: 197 VKHDPSLLEAASDLGSSTFNSFWKITVPLSKNGIVAGCMLVFIPVVGEFVIPELLGGPET 256 Query: 268 IMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSV 313 +MIG+VLWQEFFNNRDWPVASA+A++ML +LIVPI+ F++ Q K + Sbjct: 257 LMIGKVLWQEFFNNRDWPVASALAVVMLAILIVPIILFNRSQAKEM 302 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: 329 Number of extensions: 12 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: 306 Length adjustment: 27 Effective length of query: 290 Effective length of database: 279 Effective search space: 80910 Effective search space used: 80910 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