Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate 3607644 Dshi_1053 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__Dino:3607644 Length = 305 Score = 126 bits (317), Expect = 5e-34 Identities = 78/257 (30%), Positives = 138/257 (53%), Gaps = 5/257 (1%) Query: 6 VGWLVLFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLLDPLYFEVLLHSLNMALIA 65 + ++V+F LP + + SF R +++ FTL +Y E L S+ + +A Sbjct: 36 LAFMVVFFALPMALTVVFSFFERT-MFWMEPGFTLFSYNNFFFSARLENFLVSMKYSALA 94 Query: 66 TLACLVLGYPFAWFLAK-LPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYLNEFL 124 + C VLG+P A F+ + +P + ++ L I+PF + +IR++ L+ L G +N L Sbjct: 95 VVICFVLGFPVAVFIRRSIPQVAQHRVILLFILPFMVSEIIRVFALRPVLQRNGLINSTL 154 Query: 125 LWLGVIDTPIR-IMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGASKLQ 183 + G+ID PI +++T + V+IG V LPF+V + ++E + K + E DLG + Sbjct: 155 MDWGLIDEPITALLYTHTGVVIGEVLSFLPFIVFAGFLAMEAVPKFIFEVCDDLGVGHRR 214 Query: 184 TFIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDWPFG 243 F II+PL PGI AG + + + +G+ + +++GG + G +I Q + D+P Sbjct: 215 RFTDIILPLAAPGIFAGAVFIFVNGLGVALLPNILGGPGAVNAG-LIATQAITALDFPLA 273 Query: 244 AATS-ITLTIVMGLMLL 259 A S I + +MGL+ + Sbjct: 274 MAVSAIMMATLMGLLYI 290 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: 248 Number of extensions: 21 Number of successful extensions: 4 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: 305 Length adjustment: 26 Effective length of query: 249 Effective length of database: 279 Effective search space: 69471 Effective search space used: 69471 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: 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