Align putrescine transport system permease protein PotH (characterized)
to candidate WP_090446626.1 BLS63_RS16465 ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >NCBI__GCF_900100495.1:WP_090446626.1 Length = 410 Score = 179 bits (453), Expect = 1e-49 Identities = 84/216 (38%), Positives = 140/216 (64%), Gaps = 1/216 (0%) Query: 91 DDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIR 150 D +Y Y ++L +A + T C L+GYPLA+ +A + N+LL+LV+LP WTS L+R Sbjct: 184 DTQIYLQLYSKTLNMALVITLFCALLGYPLAYYLAGLPENRANLLLVLVLLPFWTSLLVR 243 Query: 151 VYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRI 210 AW+ +L+ NGV+N+FLL G+I +P +L+T+ A I + + +PFM+LP+Y+ + I Sbjct: 244 TTAWIALLQTNGVINSFLLSSGLIGEPFEMLYTSFATVIAMTHILLPFMILPLYSVMRGI 303 Query: 211 DYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIMI 270 D S + AAL LGA+P+ F + P+T G+ AG++LVFI +VG ++ P L+GG D MI Sbjct: 304 DPSYLRAALSLGAKPIPAFARIYFPMTLPGLSAGALLVFIISVGYYITPALVGGTDGQMI 363 Query: 271 GRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFH 306 ++ + +W +A+A+ ++L L+++ + W + Sbjct: 364 SNIIAFHMQRSNNWELAAALGSLLLALILI-LYWLY 398 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: 337 Number of extensions: 15 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: 410 Length adjustment: 29 Effective length of query: 288 Effective length of database: 381 Effective search space: 109728 Effective search space used: 109728 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: 49 (23.5 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