Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate SMc02738 SMc02738 glycine betaine transport system permease ABC transporter protein
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Smeli:SMc02738 Length = 281 Score = 215 bits (548), Expect = 1e-60 Identities = 120/264 (45%), Positives = 166/264 (62%), Gaps = 3/264 (1%) Query: 62 IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAII--VFALIAWQ 119 IP+ +W +DW+ T+F F + + I++ +L P P+ II V AL W Sbjct: 9 IPIGAWAKSFVDWLTTNFNLFFDQLANVLSAIISVLLYILQ-TPHPLIIIAVVTALAWWF 67 Query: 120 ISGVGMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKI 179 +G+ T + L+ I G W + TLALVL A + +G+P GI AR I Sbjct: 68 RRSLGIAAFTCLGLLLIVNQGYWQETTETLALVLAATFVSMAVGVPFGIAAARRAWIYSI 127 Query: 180 IRPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIE 239 +RP+LD MQT P FVYL+P ++LFG+G VPG++ T+IFA+P IRLT LGI P L+E Sbjct: 128 MRPILDLMQTIPTFVYLIPALILFGLGVVPGLIATVIFAIPAPIRLTRLGIISTPPALVE 187 Query: 240 ASRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIG 299 A+ SFGA+P Q+L KV+LP AMP IMAG+ QT+ML+LSMVVIA+++ GLG VLR + Sbjct: 188 AAESFGATPWQVLRKVELPFAMPQIMAGLTQTIMLSLSMVVIAALVGADGLGVPVLRALN 247 Query: 300 RLDMGLATVGGVGIVILAIILDRL 323 +++ G+ IVILAI+LDRL Sbjct: 248 TVNIARGFESGLCIVILAIVLDRL 271 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: 313 Number of extensions: 22 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: 281 Length adjustment: 27 Effective length of query: 327 Effective length of database: 254 Effective search space: 83058 Effective search space used: 83058 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