Align putrescine transport system permease protein PotH (characterized)
to candidate WP_005808911.1 DHAF_RS12790 ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >NCBI__GCF_000021925.1:WP_005808911.1 Length = 274 Score = 203 bits (517), Expect = 3e-57 Identities = 106/273 (38%), Positives = 168/273 (61%), Gaps = 19/273 (6%) Query: 29 RKLVIALPYI-WLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFL 87 +K ++ PY+ W+++ ++P ++V SL E +T + L Sbjct: 2 KKKLLTAPYLLWMLIFTIVPLILVVYFSLFESGPEGIRFTAV----------------HL 45 Query: 88 QLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSF 147 + +P+Y L+S+ +A IST CLL+GYP+A +A R+ L++L +LP W +F Sbjct: 46 ERVFEPIYLKVILRSIWLALISTVFCLLLGYPMAMILASKGLKRRDFLIVLFVLPMWMNF 105 Query: 148 LIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTAL 207 L R YAWM +L+N G++N L L + L IL+T+ AV +G+VY ++PFMVLPIY+ L Sbjct: 106 LARTYAWMTLLENKGIINQLLAALSL--PALNILYTDKAVILGMVYNFLPFMVLPIYSVL 163 Query: 208 IRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDS 267 +ID+SL+EAA DLGA P KTFF V PL+ G+ +G ++VF+PAV FVI LLGG Sbjct: 164 QKIDHSLIEAAEDLGATPYKTFFKVTFPLSLSGVASGIIMVFMPAVTTFVISRLLGGGQY 223 Query: 268 IMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIV 300 ++IG ++ Q+F DW S++++I+++ L++ Sbjct: 224 MLIGNLIEQQFLTTGDWGFGSSLSLILMIFLLL 256 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: 11 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: 274 Length adjustment: 26 Effective length of query: 291 Effective length of database: 248 Effective search space: 72168 Effective search space used: 72168 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