Align Putrescine transport system permease protein PotI (characterized)
to candidate WP_011650520.1 RL_RS04015 ABC transporter permease subunit
Query= SwissProt::P0AFL1 (281 letters) >NCBI__GCF_000009265.1:WP_011650520.1 Length = 272 Score = 293 bits (751), Expect = 2e-84 Identities = 154/271 (56%), Positives = 195/271 (71%), Gaps = 6/271 (2%) Query: 11 WRIVILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLT 70 + I+ + LGF FLY P+++LVI+SFN SKLVTVW G+ST+WY LL + ++ A +++ Sbjct: 7 FNIISVTLGFAFLYLPIVLLVIFSFNESKLVTVWGGFSTKWYVSLLSNQGLLDAAWVTIR 66 Query: 71 IAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAH 130 + +AT A ILGT+AA+ LVR+ RFRG F+ MI APLVMPDVITGLSLLLLFVA+ Sbjct: 67 VGLLSATLATILGTMAALTLVRYTRFRGRMLFSGMIYAPLVMPDVITGLSLLLLFVAIGF 126 Query: 131 AIGWPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITL 190 DRG TI LAH T +VAVV+ SRL D+SIEEAA DLGA P++ FF ITL Sbjct: 127 ------DRGFWTITLAHTTLTMCFVAVVVQSRLLSFDQSIEEAAQDLGAPPVRTFFEITL 180 Query: 191 PMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLIL 250 P+I PA++SGW+LAFTLSLDDLVIASF SGPGATTLPM ++S VR+GV PEINA+ T+++ Sbjct: 181 PIIAPAVLSGWILAFTLSLDDLVIASFTSGPGATTLPMRIYSQVRLGVTPEINAVCTILI 240 Query: 251 GAVGIVGFIAWYLMARAEKQRIRDIQRARRG 281 V + A + R E QR RD + A G Sbjct: 241 AIVTVGVICASVVTKRREIQRQRDERAAAAG 271 Lambda K H 0.330 0.140 0.430 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: 272 Number of extensions: 14 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: 281 Length of database: 272 Length adjustment: 25 Effective length of query: 256 Effective length of database: 247 Effective search space: 63232 Effective search space used: 63232 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 (21.9 bits) S2: 47 (22.7 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