Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate AZOBR_RS15765 AZOBR_RS15765 osmoprotectant uptake system permease
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__azobra:AZOBR_RS15765 Length = 390 Score = 122 bits (305), Expect = 2e-32 Identities = 76/244 (31%), Positives = 133/244 (54%), Gaps = 15/244 (6%) Query: 93 ILNGFQQLLLGMPAPVAI--IVFALIAWQISGVGMGVATLVSLIAIGAIGAWSQAMVTLA 150 +L+G ++L LG VA+ + ALI Q + + +++ A + A Sbjct: 128 VLDGVRRLELGPAGRVAVGALAAALIGGQFAAGHLDQLSIMKEYANQRDVFAGAVLRHAA 187 Query: 151 LVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDAMQTTPAF----VYLVPIVMLF--- 203 LV AL+ ++IG+PLGI RS +++ P+L+ +QT P+ + L P+ L Sbjct: 188 LVAAALVPTLLIGVPLGIAAQRSAAVGRLVFPVLNVVQTIPSIALFGLLLAPLSALAAAF 247 Query: 204 ------GIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLFKVQL 257 G+G VP V+ +++L PI R T G+ VP + EA+R G +PRQ+ ++V+ Sbjct: 248 PGLGIGGVGPVPAVIALTLYSLLPIARNTAAGLAGVPEPVREAARGIGMTPRQIFWRVEA 307 Query: 258 PLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLATVGGVGIVILA 317 PLA+P +AG+ TL+ A+ + +A++I GGLG ++ +G+ + L +G V +++LA Sbjct: 308 PLALPVFLAGLRITLVQAVGLAAVAALIGAGGLGAIMFQGLFANALDLVLLGAVPVILLA 367 Query: 318 IILD 321 + D Sbjct: 368 VAAD 371 Lambda K H 0.326 0.141 0.435 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: 360 Number of extensions: 26 Number of successful extensions: 2 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: 354 Length of database: 390 Length adjustment: 30 Effective length of query: 324 Effective length of database: 360 Effective search space: 116640 Effective search space used: 116640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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