Align Ectoine/glycine betaine/proline transporter EctP (characterized)
to candidate WP_075844956.1 BJL86_RS10330 BCCT family transporter
Query= SwissProt::Q79VE0 (615 letters) >NCBI__GCF_001659785.1:WP_075844956.1 Length = 725 Score = 319 bits (818), Expect = 2e-91 Identities = 172/504 (34%), Positives = 283/504 (56%), Gaps = 18/504 (3%) Query: 25 IFSISVGFIVVFVIATIALGEKARTTFSAIAGWLLENLGWMYIGGVSLVFIFLMGIFASR 84 +F+ + IV FV+ + A T W+ N GW YI ++V +F++ + SR Sbjct: 36 VFAGTSVIIVAFVLWAAIWPDAASTAIFGAMDWVATNFGWYYILTATIVVVFVIVVAFSR 95 Query: 85 YGRVKLGDDDDDPEHTLIVWFCMLFAGGVGAVLMFWGVAEPINHAFNVPMANEESMSEAA 144 GR K+G D P+ L W MLFA G+G LMF+G++ P + P +MS+ A Sbjct: 96 VGRTKMGPDHSRPKFNLFTWAAMLFAAGIGVDLMFFGISGPATNYLTPPDVG--AMSDEA 153 Query: 145 IVQAFAYTFYHFGIHMWVIMALPGLSLGYFIYKRKLPPRLSSVFSPILGKHIYSTPGKLI 204 A +T +H+GI W + AL G++ G F Y+ LP + S +PI GK I+ G + Sbjct: 154 ARMAPIWTIFHYGIPGWAMYALMGMAFGLFAYRYHLPLSIRSALAPIFGKRIHGAAGHTV 213 Query: 205 DVLAIVGTTFGIAVSVGLGVLQINAGMNKLWSTPQVSWVQLLIILIITAVACISVASGLD 264 ++ A +GT FGI+VS+G+GV+ +N G+++L+ P VQ+ ++ + + S SG+D Sbjct: 214 EIAATIGTIFGISVSLGIGVVFLNYGLSELFGVPNSLSVQIALMALAVFITIASTVSGVD 273 Query: 265 KGIKLLSNINIAMAVALMFFILFTGPTLTLLRFLVESFGIYASWMPNLMFWTDSFQ---- 320 KGI+ LS +N+ +A+ L ++LF+G T +L LV++ G + S P++M T ++ Sbjct: 274 KGIRRLSELNVILAIVLALWVLFSGQTAHMLDALVQNIGDFFSRFPSMMMNTFAYSTGTA 333 Query: 321 DNPG--WQGKWTVFYWAWTICWSPYVGMFVARISRGRTVREFIGGVLALPAIFGVVWFSI 378 D P W+ WT+F+WAW I W+P+V +F+ARISRGRT+R+F+ GVL +P F ++W SI Sbjct: 334 DYPAEQWKADWTLFFWAWWIAWAPFVSLFLARISRGRTLRQFVIGVLLIPFSFILMWVSI 393 Query: 379 FGRAGIEVELSNPGFLTQPTVVEGDVPAALFNVLQEYPLTGIVSAFALVIIVIFFITSID 438 FG A + + FL Q + + F +L++YP + + A++ + F++TS D Sbjct: 394 FGNAALSF-FDDQEFLNQAVELP---ESGFFTLLEQYPGSTFTISIAVLTGMFFYVTSAD 449 Query: 439 SAALVNDMFA---TGAENQTPTSYRVMWACTIGAVAGSLLIISPSSGIATLQEVVIIVAF 495 S +LV T ++ P R++WA GA+ +L I G+ TLQ ++V Sbjct: 450 SGSLVMANMTSKPTMNDSDGPPWLRIVWAVITGALTLVMLFI---DGVYTLQAATVMVGL 506 Query: 496 PFFLVQFVMMFSLLKGMSEDAAAV 519 P ++ +++MFSL K + + + Sbjct: 507 PLSILIYLVMFSLWKVLKTEQLGI 530 Lambda K H 0.324 0.140 0.434 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: 1120 Number of extensions: 58 Number of successful extensions: 4 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: 615 Length of database: 725 Length adjustment: 38 Effective length of query: 577 Effective length of database: 687 Effective search space: 396399 Effective search space used: 396399 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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