Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate GFF3355 HP15_3297 binding-protein-dependent transport systems inner membrane component
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Marino:GFF3355 Length = 344 Score = 201 bits (511), Expect = 2e-56 Identities = 106/246 (43%), Positives = 166/246 (67%), Gaps = 14/246 (5%) Query: 89 PVDYILNGFQQLLLG------MPAPVAIIVFALIAWQISGVGMGVATLVSLIAIGAIGAW 142 P+ + L+G +L +P +A++ +W++ G S++ + I + Sbjct: 94 PLSWFLDGALYAMLNTPWWIVIPLLLAVVYVVTKSWKLMLFVGG-----SIVLLAFIDHY 148 Query: 143 SQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDAMQTTPAFVYLVPIVML 202 AM TLA++ C+++G+P+GI +ARS ++I P+LD +QT P FVYL+P++ L Sbjct: 149 DYAMQTLAIIFVCAFLCVLLGVPIGIAMARSNSLQRMIIPVLDMLQTLPPFVYLIPLIFL 208 Query: 203 FGI--GNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLFKVQLPLA 260 F + + G+ + I++A+ P+IRLT LGI V D+IEA+ +FG +PRQ L+KVQ+PLA Sbjct: 209 FSVTESKLYGIAI-ILYAIVPVIRLTNLGIRLVDKDVIEAADAFGMTPRQKLYKVQIPLA 267 Query: 261 MPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLATVGGVGIVILAIIL 320 +P IMAGVNQT+M++L+MVVIAS+++ GLG +VLRGI L++G+ V G+GIVILA+IL Sbjct: 268 LPNIMAGVNQTIMMSLAMVVIASLVSAPGLGVLVLRGIRNLELGVGLVSGLGIVILAVIL 327 Query: 321 DRLTQA 326 DR+T+A Sbjct: 328 DRVTKA 333 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: 344 Number of extensions: 14 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: 344 Length adjustment: 29 Effective length of query: 325 Effective length of database: 315 Effective search space: 102375 Effective search space used: 102375 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