Align putrescine transport system permease protein PotH (characterized)
to candidate BPHYT_RS23140 BPHYT_RS23140 putrescine/spermidine ABC transporter permease
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__BFirm:BPHYT_RS23140 Length = 324 Score = 345 bits (884), Expect = 1e-99 Identities = 166/317 (52%), Positives = 233/317 (73%), Gaps = 6/317 (1%) Query: 2 STLEPAAQSKPPGG-----FKLWLSQLQMKHGRKLVIALPYIWLILLFLLPFLIVFKISL 56 +T PAA P G K LS L + GR VI +P++WL + F LPF++V KIS Sbjct: 5 TTSSPAALGAPSGSRLLGSLKKRLSML-VPSGRSTVIGVPFLWLTVFFALPFVLVLKISF 63 Query: 57 AEMARAIPPYTELMEWADGQLSITLNLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLI 116 A++ IPPYT+L+ DG + + L ++ L D LY Y+ SL++AA+STF CLLI Sbjct: 64 ADLRLGIPPYTDLVTVKDGMVHFAMQLSHYAFLLQDDLYVATYISSLKMAAVSTFFCLLI 123 Query: 117 GYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQ 176 GYP+A+ +A S+P+ RN+L++ V+LP WTSFLIRVYAW+GILK++G+LN+ L+ +G+I Sbjct: 124 GYPIAYYIARSEPTKRNLLMMGVMLPFWTSFLIRVYAWIGILKDDGLLNHTLMAIGMIHS 183 Query: 177 PLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPL 236 PL + HT++ VYIG+VY+Y+PFMV+P+Y L+++D +L+EAA DLG +P F + +PL Sbjct: 184 PLRLYHTDIGVYIGMVYSYLPFMVMPLYAHLVKMDLTLLEAAYDLGCKPWTAFTRITLPL 243 Query: 237 TKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLL 296 +K GIIAGS+LVFIPAVGE+VIPELLGG D++MIGRV+W EFFN+ DWP+ASAV + M+L Sbjct: 244 SKNGIIAGSLLVFIPAVGEYVIPELLGGADTLMIGRVMWDEFFNDMDWPMASAVTVAMVL 303 Query: 297 LLIVPIMWFHKHQQKSV 313 LL+VP+ F +Q K + Sbjct: 304 LLLVPMAVFQYYQVKEL 320 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: 374 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: 324 Length adjustment: 28 Effective length of query: 289 Effective length of database: 296 Effective search space: 85544 Effective search space used: 85544 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