Align proline porter II (characterized)
to candidate GFF2891 PS417_14785 glycine/betaine ABC transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__WCS417:GFF2891 Length = 500 Score = 832 bits (2150), Expect = 0.0 Identities = 404/498 (81%), Positives = 458/498 (91%) Query: 2 LKRKKVKPITLRDVTIIDDGKLRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADP 61 L++K VKPI L+D+TI+DD K+RKAITAA+LGNAMEWFDFGVYGFVAY LGKVFFP A P Sbjct: 3 LRKKSVKPIGLKDITIVDDTKVRKAITAAALGNAMEWFDFGVYGFVAYVLGKVFFPDASP 62 Query: 62 SVQMVAALATFSVPFLIRPLGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDT 121 SVQM+AAL TFSVPFLIRPLGGLFFG LGDKYGRQK+LA TIVIMS+STF IGLIPSY + Sbjct: 63 SVQMIAALGTFSVPFLIRPLGGLFFGALGDKYGRQKVLAATIVIMSLSTFAIGLIPSYAS 122 Query: 122 IGIWAPILLLICKMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAG 181 IGIWAPILLL+CKMAQGFSVGGEYTGASIFVAEY+PDRKRGF+GSWLDFGSIAGFVLGAG Sbjct: 123 IGIWAPILLLLCKMAQGFSVGGEYTGASIFVAEYAPDRKRGFLGSWLDFGSIAGFVLGAG 182 Query: 182 VVVLISTIVGEANFLDWGWRIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREG 241 VVVLIS+I+GEA+F WGWR+PFF+ALPLGIIGLYLRHALEETPAFQQH+DK+EQGDREG Sbjct: 183 VVVLISSILGEADFESWGWRLPFFLALPLGIIGLYLRHALEETPAFQQHMDKMEQGDREG 242 Query: 242 LQDGPKVSFKEIATKYWRSLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLII 301 L GPKVSFKE+ATK+WRSLLTCIG+V ATNVTYYMLLTYMPSYLSHNLHY E+ GVLII Sbjct: 243 LTHGPKVSFKEVATKHWRSLLTCIGIVAATNVTYYMLLTYMPSYLSHNLHYKENSGVLII 302 Query: 302 IAIMIGMLFVQPVMGLLSDRFGRRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLML 361 IAIM+GMLFVQP +G +SD+ GR+PF++ GS+ L L+IPAF+LI S IGLIFAGLL+L Sbjct: 303 IAIMVGMLFVQPFIGFISDKIGRKPFIIAGSIGLLFLSIPAFMLITSGKIGLIFAGLLIL 362 Query: 362 AVILNCFTGVMASTLPAMFPTHIRYSALAAAFNISVLVAGLTPTLAAWLVESSQNLMMPA 421 AVILN F GVMASTLPAMFPTH+RYSALA+AFN+SVL+AGLTPT AWLVES+ +L MPA Sbjct: 363 AVILNFFIGVMASTLPAMFPTHLRYSALASAFNVSVLIAGLTPTAVAWLVESTNDLYMPA 422 Query: 422 YYLMVVAVVGLITGVTMKETANRPLKGATPAASDIQEAKEILVEHYDNIEQKIDDIDHEI 481 YYLMV AVVGLITG+TMKETAN+PL+GA PAASD++EAKE+L EH+DNIEQKI+DID EI Sbjct: 423 YYLMVFAVVGLITGLTMKETANKPLRGAAPAASDMEEAKELLQEHHDNIEQKIEDIDAEI 482 Query: 482 ADLQAKRTRLVQQHPRID 499 A+L+AKR LV+QHPRI+ Sbjct: 483 AELEAKRKNLVEQHPRIN 500 Lambda K H 0.327 0.142 0.429 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: 994 Number of extensions: 40 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: 500 Length of database: 500 Length adjustment: 34 Effective length of query: 466 Effective length of database: 466 Effective search space: 217156 Effective search space used: 217156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 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