Align Putrescine transport system permease protein PotI (characterized)
to candidate SMc01634 SMc01634 ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__Smeli:SMc01634 Length = 272 Score = 179 bits (454), Expect = 6e-50 Identities = 107/258 (41%), Positives = 161/258 (62%), Gaps = 16/258 (6%) Query: 20 FTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAACAATAA 79 + FLYAP+ ++V++SFN+ + + + G+S WYG+ L + ++SA+ SL IA +AT A Sbjct: 9 YLFLYAPIALVVLFSFNAGRNASEFTGFSLAWYGKALGNTFLVSALQNSLIIAFTSATLA 68 Query: 80 AILGTIAAVVLVRFG-RFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIG----- 133 A+ GT+AA+ + R G R R F + A +V+P V+ G++ L+ VA+ + Sbjct: 69 AVFGTMAALGMERLGSRMRAL--FDALFAAAIVVPGVVIGIATLVALVAVFSFVNPTIAA 126 Query: 134 -WPADR------GMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFF 186 WP ++ G +I AH F A V +++ +R+ L R I EA+ DL ATPL F Sbjct: 127 LWPGEQPPQLGLGYGSIIAAHGLFSMALVTMIVKARIASLGRDIVEASGDLYATPLTTFR 186 Query: 187 VITLPMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALA 246 +I LP I+P+I++G+LLAFT S DD +IA FV+G TTLP+ VF+S+R GV PEINA+A Sbjct: 187 LIVLPQILPSILAGFLLAFTFSFDDFIIAFFVAG-SKTTLPIYVFASIRRGVTPEINAIA 245 Query: 247 TLILGAVGIVGFIAWYLM 264 TL+L A ++ A LM Sbjct: 246 TLVLVASLLLILTARVLM 263 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: 207 Number of extensions: 9 Number of successful extensions: 3 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 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