Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate 3608194 Dshi_1599 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__Dino:3608194 Length = 293 Score = 183 bits (465), Expect = 3e-51 Identities = 101/255 (39%), Positives = 162/255 (63%), Gaps = 5/255 (1%) Query: 10 VLFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLL-DPLYFEVLLHSLNMALIATLA 68 +L + +P + I+ SF T++ F + FTL NY + DP+Y ++ SL +A + T+ Sbjct: 28 ILLLAVPLVAILVLSFWTQNFMEFDRS-FTLANYREAVTDPIYGTLMGRSLWIAGMVTVV 86 Query: 69 CLVLGYPFAWFLA-KLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYLNEFLLWL 127 +VL +P A+F++ +P + L +FL+ VPFWT+ L+R++ K+ L G LN L L Sbjct: 87 TVVLAFPIAYFVSFHVPQNRKALWIFLITVPFWTSYLLRVFLWKVILGFNGVLNSGLQGL 146 Query: 128 GVIDTPIR-IMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGASKLQTFI 186 G+I+ P+ +++ +AV+I L + PF ++P+Y ++EK+D+ LLEAARDLG S F Sbjct: 147 GIIEEPLTFLLYNANAVVITLAHAYAPFTILPIYVALEKIDRSLLEAARDLGESAWGAFC 206 Query: 187 RIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDWPFGAAT 246 RI +PL MPGI+A L+V +P +G + L+GG L+I N+I+ QFL + D P GAA Sbjct: 207 RITLPLAMPGIVAATLIVFIPVIGDYVTPRLVGGPDGLMIANMIQTQFLRLNDAPMGAAL 266 Query: 247 SIT-LTIVMGLMLLV 260 +++ +TIV + LLV Sbjct: 267 AVSAMTIVSAIALLV 281 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: 265 Number of extensions: 17 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: 293 Length adjustment: 26 Effective length of query: 249 Effective length of database: 267 Effective search space: 66483 Effective search space used: 66483 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