Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate GFF1153 HP15_1130 transporter, BCCT family protein
Query= SwissProt::Q87PP5 (562 letters) >FitnessBrowser__Marino:GFF1153 Length = 530 Score = 630 bits (1626), Expect = 0.0 Identities = 295/511 (57%), Positives = 396/511 (77%), Gaps = 2/511 (0%) Query: 48 TTDYQVGQDNVQKWGFDIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQF 107 +TDY GQDN+ +G D+H PVF I+A ++VF + L+ P A++ L+G K II F Sbjct: 10 STDYVAGQDNITPFGLDLHAPVFPITA-ILVFAFVIGTLMFPGEAKELLDGTKWDIIATF 68 Query: 108 DAFFMWSTNFFLLFAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSV 167 D FF+ S N F++ + L+F P+GKIR+GG++ P+ ST+SW MLFAAGMGIGL+FW+V Sbjct: 69 DWFFLISANIFVVVCLALIFLPMGKIRIGGQDCKPEFSTISWFCMLFAAGMGIGLMFWAV 128 Query: 168 AEPTAYFTDWWGTPLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGL 227 AEP AY+T W+ TPLN EA + +A++LAMGATM+HWG+H W IYA+VAL+LAFFAFNK + Sbjct: 129 AEPVAYYTGWYETPLNVEAGTNEARNLAMGATMYHWGLHPWGIYAIVALSLAFFAFNKNM 188 Query: 228 PLSLRAAFYPIFGDRAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGG 287 PL++R+AF+P+ D+ WGW GH+ID+LAV++T+FGLATSLG GAQQA SG+N++FG+ G Sbjct: 189 PLTIRSAFFPLLRDKVWGWPGHIIDVLAVVATIFGLATSLGFGAQQAASGLNYLFGIGAG 248 Query: 288 IGTQMVVIAFVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFI-TFDTAMGSLVD 346 I QM +I VT +A++SV+RG+DGGVK+LSN+NM VA LL+F+ F T + +L Sbjct: 249 INVQMAIIVGVTALALISVLRGLDGGVKVLSNINMGVAAVLLLFVIFAGPTMTILETLWV 308 Query: 347 TTMAYIQNIIPLSNPHGREDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLF 406 T+ Y+ N + LSNP GREDE W GWTVFYWAWW+SWSPFVGMFIARVSKGRTVREF+ Sbjct: 309 TSSNYVGNAVQLSNPFGREDEAWFQGWTVFYWAWWISWSPFVGMFIARVSKGRTVREFVT 368 Query: 407 AVIVIPTLVTLVWMSVFGGIALDQVVNKVGELGANGLTDISLTLFHVYDVLPYSSVISIL 466 AV+++PT++T+VWMS FGG A++Q+ VGEL NGLT++SL F ++ LP + ++S + Sbjct: 369 AVLIVPTVITVVWMSAFGGAAIEQIQQGVGELAENGLTEVSLATFQMFANLPLTGILSFV 428 Query: 467 SIVLILVFFITSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEALQ 526 I+L+LVFF+TSSDSGSLVIDSITAGGK DAP QR+FW EG+IAA +++ GG++AL Sbjct: 429 GIILVLVFFVTSSDSGSLVIDSITAGGKTDAPTAQRVFWVVAEGAIAAALIFGGGEDALG 488 Query: 527 ALQSGVVATGLPFTFVLLLMCVSLVKGLRTE 557 A+Q+ ++ GLPFT VLL+M L+KGL E Sbjct: 489 AIQATAISAGLPFTVVLLIMTWGLLKGLSHE 519 Lambda K H 0.327 0.141 0.445 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: 1021 Number of extensions: 54 Number of successful extensions: 3 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: 562 Length of database: 530 Length adjustment: 35 Effective length of query: 527 Effective length of database: 495 Effective search space: 260865 Effective search space used: 260865 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