Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate AZOBR_RS11810 AZOBR_RS11810 ABC transporter permease
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__azobra:AZOBR_RS11810 Length = 267 Score = 67.0 bits (162), Expect = 5e-16 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 5/192 (2%) Query: 128 ATLVSLIAIGAIGA-WSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDA 186 A +L A+ G+ W +L + + V G+ +G + A + PL+ A Sbjct: 58 AVASALAAMAQDGSLWQHLKASLMRIGVGWVMGTVAGMAVGFAMGIGSVARAVGVPLVSA 117 Query: 187 MQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALP-PIIRLTILGINQVPADLIEASRSFG 245 P L ++ FGIG P TI F + P + T I+ VP +LI ++SFG Sbjct: 118 FFPIPKIALLPLFILWFGIGE-PSKFATIGFGVFFPTVIATYSAIDSVPRNLIRMAQSFG 176 Query: 246 ASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMI-AVGGLGQMVLRGIGRLDMG 304 +L K+ LP A+P I+AG T +AL +VV A MI A G+G VL G L + Sbjct: 177 LPWASILRKIVLPGALPGILAGFRITASIALILVVAAEMIGAEYGIGAFVLTA-GNLMLT 235 Query: 305 LATVGGVGIVIL 316 + GV ++ L Sbjct: 236 DQLLAGVLVLSL 247 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: 248 Number of extensions: 15 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: 267 Length adjustment: 27 Effective length of query: 327 Effective length of database: 240 Effective search space: 78480 Effective search space used: 78480 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: 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