Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate SMa0800 SMa0800 ABC transporter permease
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__Smeli:SMa0800 Length = 291 Score = 169 bits (429), Expect = 5e-47 Identities = 87/249 (34%), Positives = 147/249 (59%), Gaps = 9/249 (3%) Query: 6 VGWLVLFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLL-DPLYFEVLLHSLNMALI 64 +G L+LF LP M+ LTR S + V L NY LL Y + ++ ++ + Sbjct: 31 LGLLILFFVLPVAML-----LTR---SVTEPVPGLGNYAELLGSSTYLRIFANTFIVSSL 82 Query: 65 ATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYLNEFL 124 TL L++G+P AW LA +P + ++ +L++ WTN L R Y + L G +N+ L Sbjct: 83 VTLVSLLIGFPVAWALAIMPSRAASIVFAILLLSMWTNLLARTYAWMVLLQRTGVINKML 142 Query: 125 LWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGASKLQT 184 L +G+IDTP+ ++ + V IG+ YI+LPF+++PLY I K+D +L+AA GA++ Q+ Sbjct: 143 LGMGLIDTPLPLVNNLTGVTIGMTYIMLPFIILPLYGVIRKIDPAILQAAALCGANRWQS 202 Query: 185 FIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDWPFGA 244 +R+++PL MPG+ AG L+V + ++G F L+GG N+++ +I ++ +W G Sbjct: 203 LVRVLLPLAMPGMAAGALMVFVMSLGYFVTPALLGGTSNMMLAELIAQFVQSLVNWGMGG 262 Query: 245 ATSITLTIV 253 A ++ L +V Sbjct: 263 AAALVLLVV 271 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: 268 Number of extensions: 11 Number of successful extensions: 1 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: 291 Length adjustment: 26 Effective length of query: 249 Effective length of database: 265 Effective search space: 65985 Effective search space used: 65985 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