Align putrescine transport system permease protein PotH (characterized)
to candidate WP_009565322.1 RSPH17029_RS08335 ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >NCBI__GCF_000015985.1:WP_009565322.1 Length = 295 Score = 176 bits (447), Expect = 5e-49 Identities = 105/290 (36%), Positives = 168/290 (57%), Gaps = 20/290 (6%) Query: 20 LSQLQMKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSI 79 L + + HG L++ P ++ ILL P I Y+ L DG L I Sbjct: 10 LRRSEAAHGY-LLVGPPALYAILLLAAPL------------GTIAVYSFL---TDGYLEI 53 Query: 80 T--LNLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVA-HSKPSTRNILL 136 L N+ + + LY L+SL VA T +++ +P+A+ V+ H P +++ L Sbjct: 54 IREFTLANYHEAWTNELYRTVMLRSLGVAMAVTAVTVVLAFPVAYFVSFHVAPERKSLWL 113 Query: 137 LLVILPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNL-AVYIGIVYAY 195 L+ +P WTS+LIRV+ W IL NGV+N+ LL LG+ID+PLT + N+ AV I + +AY Sbjct: 114 FLITIPFWTSYLIRVFLWKVILGFNGVINSGLLGLGIIDEPLTFILYNVNAVVITLAHAY 173 Query: 196 VPFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGE 255 PF +LPI+ AL +ID +L+EA DLG L TF+ V +PL G+IA ++VFIP +G+ Sbjct: 174 APFAILPIFVALEKIDRALLEAGQDLGESKLMTFWRVTLPLAMPGVIASVLIVFIPTIGD 233 Query: 256 FVIPELLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWF 305 +V P+L+GGP+ M+ ++ ++ ++P+ SA+A+ + ++ V + F Sbjct: 234 YVTPQLVGGPEGRMVANLIQLQYLKLDNYPLGSAIAVSAMSIVTVVSLIF 283 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: 264 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: 295 Length adjustment: 27 Effective length of query: 290 Effective length of database: 268 Effective search space: 77720 Effective search space used: 77720 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 Apr 10 2024. 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