Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate GFF3384 PGA1_c34370 spermidine/putrescine transport system permease protein PotB
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__Phaeo:GFF3384 Length = 423 Score = 161 bits (407), Expect = 3e-44 Identities = 79/221 (35%), Positives = 132/221 (59%), Gaps = 5/221 (2%) Query: 50 LYFEVLLHSLNMALIATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYG 109 +Y + L +L M+L T++C+VLGYP AW LA LP + LL+ L+++PFWT+ L+R Sbjct: 198 IYGTLFLRTLIMSLAITVSCIVLGYPVAWILANLPSRTANLLMILVLLPFWTSLLVRTSA 257 Query: 110 LKIFLSTKGYLNEFLLWLGVIDTPIRIMFTPS--AVIIGLVYILLPFMVMPLYSSIEKLD 167 K+ L +G +N+ L+WLG++ R++ + I+ + +ILLPFM++P+YS ++ ++ Sbjct: 258 WKVMLQQQGVINDTLVWLGLVADDARLVMINNQFGTIVAMTHILLPFMILPMYSVMQTIN 317 Query: 168 KPLLEAARDLGASKLQTFIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIG 227 L AA+ LGA+ F R+ P ++PGI AG +LV + A+G + +L+GG K + I Sbjct: 318 PSYLRAAKSLGATNWTAFWRVYFPQSVPGIGAGSILVFILAIGYYITPELVGGTKGVFIS 377 Query: 228 NVIKVQFLNIRDWPFGAATSITLTIVMGLMLLVYWRASRLL 268 N I +W AA L +V +L +YW +++ Sbjct: 378 NRIAFHISQSLNWGLAAALGSILLVV---VLALYWAYDKIV 415 Lambda K H 0.333 0.148 0.456 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: 339 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 275 Length of database: 423 Length adjustment: 28 Effective length of query: 247 Effective length of database: 395 Effective search space: 97565 Effective search space used: 97565 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 49 (23.5 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