Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate 3608029 Dshi_1436 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Dino:3608029 Length = 513 Score = 209 bits (531), Expect = 2e-58 Identities = 107/260 (41%), Positives = 162/260 (62%) Query: 66 SWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQISGVGM 125 +WV + I W V + F + + +L+ + +L+ P V + L+ W +G+ Sbjct: 250 AWVEDFIAWTVRNTEAFFDALTFGIRTLLDALEVILVQTPWIVIASLIVLLTWLTAGLRT 309 Query: 126 GVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLD 185 + + L +G +G W AM TLAL+ TA IVIG+PLG++ AR PR I+P++D Sbjct: 310 AIYSSAFLAYMGLLGFWEAAMTTLALLGTAACLSIVIGIPLGMFAARRPRFYAFIQPIMD 369 Query: 186 AMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFG 245 MQT PAFV++VP++ FG+G V+VT+IF P++RLT+LG+ VP + EA+ SFG Sbjct: 370 FMQTMPAFVFMVPVIAFFGVGKPAAVIVTMIFGGTPVVRLTVLGLRGVPESVREAAISFG 429 Query: 246 ASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGL 305 A+ +L KV LPLA P+I AG+NQT+ML+L+MVV+AS+I GLG+ VL + ++G Sbjct: 430 ANKWYLLTKVDLPLAGPSIRAGINQTIMLSLAMVVVASLIGAKGLGEDVLEALQYANVGQ 489 Query: 306 ATVGGVGIVILAIILDRLTQ 325 + G I+ A+ILDR+ Q Sbjct: 490 GILAGFSILFCAMILDRIVQ 509 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: 429 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: 354 Length of database: 513 Length adjustment: 32 Effective length of query: 322 Effective length of database: 481 Effective search space: 154882 Effective search space used: 154882 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: 51 (24.3 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