Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate Pf1N1B4_3973 ABC-type spermidine/putrescine transport system, permease component I
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3973 Length = 289 Score = 163 bits (413), Expect = 3e-45 Identities = 82/250 (32%), Positives = 157/250 (62%), Gaps = 5/250 (2%) Query: 15 LPNLMIIGTSFLTRDDASFVKM-VFTLDNYTRLL-DPLYFEVLLHSLNMALIATLACLVL 72 +P L+ + SF D +S + +TLD+Y+ LL DP ++E+ L + ++ + TL C+V+ Sbjct: 30 IPLLLTLVLSFNVFDYSSGINSDAYTLDHYSSLLGDPYFYEIFLRTFWISALTTLLCVVI 89 Query: 73 GYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYLNEFLLWLGVIDT 132 G P A+ L+++ R + L L++ P + ++R +G + L G +N+ L G + Sbjct: 90 GVPEAYILSRMGTPWRSIFLILILTPLLISVVVRAFGWSLLLGADGLVNQTLQAFG--GS 147 Query: 133 PIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGASKLQTFIRIIIPL 192 P+++++TP AV+I LV+++LPFM++P+++S++KLD +AA LGAS L ++++P Sbjct: 148 PMKLLYTPFAVVIALVHVMLPFMIIPVWTSLQKLDPAAEQAALSLGASHLTVMRKVVLPQ 207 Query: 193 TMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDWPFGAATSITLTI 252 MPG+++G L+V A F + L+GG + ++ +I Q+L+ +WP GAA ++ L + Sbjct: 208 IMPGVLSGTLIVFGLAASSFAIPGLLGGRRIKMVATLIYDQYLSELNWPMGAAIAVAL-L 266 Query: 253 VMGLMLLVYW 262 ++ L++++ W Sbjct: 267 LLNLLIMLSW 276 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: 263 Number of extensions: 15 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: 275 Length of database: 289 Length adjustment: 26 Effective length of query: 249 Effective length of database: 263 Effective search space: 65487 Effective search space used: 65487 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: 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