Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SM_b21220 SM_b21220 sugar ABC transporter permease
Query= TCDB::G3LHZ0 (288 letters) >FitnessBrowser__Smeli:SM_b21220 Length = 293 Score = 127 bits (320), Expect = 2e-34 Identities = 90/288 (31%), Positives = 150/288 (52%), Gaps = 9/288 (3%) Query: 1 MQKTW-NNKAWFLVLPVLLLVAFSAVI--PLMTVVNYSVQDT-FGNNEFFWAGTDWFVQT 56 M TW + +AW L+LP LLV +AVI PL+ V S D E + GT +++ Sbjct: 1 MTGTWISTRAWLLMLP--LLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKM 58 Query: 57 LHSDRFWESLQRNLLFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIPWNVV 116 L F +L F+ I +A E+ LG+ AL + + G LM LP +P V Sbjct: 59 LGGSNFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVN 118 Query: 117 GTIWQVFGRVDIGLLGHTLEAIGLDYNY---VRDPIDAWVTVIVMDVWHWTSLVVLLCYA 173 T+W++ + G L L +GL +Y + +P A +IV D W LV L+ A Sbjct: 119 ATLWRLIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALA 178 Query: 174 GLVSIPDAYYQAAKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGG 233 L ++P A+ +DGA ++ FR++ +P + LL+A++LR +++F ++ +V+T G Sbjct: 179 ALQAVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRG 238 Query: 234 GPGNSTTFLSIDLVKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYTVM 281 GP NST LSI + + A G A++++I L++ +L+ + ++ Sbjct: 239 GPANSTRTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALL 286 Lambda K H 0.329 0.143 0.464 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: 247 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: 288 Length of database: 293 Length adjustment: 26 Effective length of query: 262 Effective length of database: 267 Effective search space: 69954 Effective search space used: 69954 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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