Align putrescine transport system permease protein PotH (characterized)
to candidate Pf1N1B4_4351 Putrescine transport system permease protein PotH (TC 3.A.1.11.2)
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4351 Length = 304 Score = 375 bits (964), Expect = e-109 Identities = 174/290 (60%), Positives = 229/290 (78%) Query: 28 GRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFL 87 GRKLVI +P++WL L FLLPF +V KIS +E A AIPPY+E+ +A+ + + LN+GN+ Sbjct: 15 GRKLVIGIPFLWLCLFFLLPFFLVMKISFSEAALAIPPYSEIYTFAEQKFQLLLNIGNYS 74 Query: 88 QLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSF 147 LT+D LY AY SL+VA +ST CL+IG+P+A+A+ + T+N+LLLL+++P+WT+ Sbjct: 75 LLTEDELYISAYFGSLKVAFLSTLMCLVIGFPMAYAITKANKETQNVLLLLIMMPTWTAI 134 Query: 148 LIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTAL 207 LIRVYAWMGIL NNG+LN FL+W G+ P+ IL+TN AVYIG+VYAY+PFMVLP+Y L Sbjct: 135 LIRVYAWMGILSNNGLLNAFLMWTGLTSHPIEILNTNTAVYIGVVYAYLPFMVLPLYANL 194 Query: 208 IRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDS 267 ++ D+SL+EAA DLG+ F+ + VPL K GIIAG MLVFIP VGEFVIPELLGGP++ Sbjct: 195 VKHDHSLLEAASDLGSSNFNNFWKITVPLAKNGIIAGCMLVFIPVVGEFVIPELLGGPET 254 Query: 268 IMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSVGEHG 317 +MIGRVLWQEFFNNRDWPVASA+A++ML +LIVPI+ F++ Q K + G Sbjct: 255 LMIGRVLWQEFFNNRDWPVASALAVVMLAILIVPILLFNRSQAKEMEGRG 304 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: 350 Number of extensions: 7 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: 304 Length adjustment: 27 Effective length of query: 290 Effective length of database: 277 Effective search space: 80330 Effective search space used: 80330 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