Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate GFF5140 PS417_26330 beta-aspartyl peptidase
Query= SwissProt::Q87PP5 (562 letters) >FitnessBrowser__WCS417:GFF5140 Length = 663 Score = 344 bits (883), Expect = 5e-99 Identities = 193/504 (38%), Positives = 300/504 (59%), Gaps = 22/504 (4%) Query: 69 VFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFAVGLLFS 128 VF S L++ L ++L++ P A L + + + F ++M +L+F VGL FS Sbjct: 20 VFYTSTALILL-LTAILIIAPQEAGRMLGVAQAWLSKSFGWYYMVVIAAYLVFVVGLAFS 78 Query: 129 PLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTPLNAEAYS 188 GK++LG K+ TPD S +W MLF++G+GI LL++ +EP D + P A S Sbjct: 79 SYGKLKLGSKDDTPDFSYGAWAGMLFSSGIGISLLYFGASEPL----DHYFNPPEGAAAS 134 Query: 189 ADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFGDRAW--GW 246 A A+ T HWG+HGW+IYALV LA+A+FA+ PL+LR+A YP+ G+R W G Sbjct: 135 NGAARQALQLTFLHWGLHGWAIYALVGLAVAYFAYRHNQPLALRSALYPLVGER-WVKGA 193 Query: 247 LGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGGIGTQMVVIAFVTFIAVLSV 306 GH +D + TL GL T+LG+G+ Q +SG+ ++FG+ ++VI ++ +A ++ Sbjct: 194 AGHAVDGFGMFVTLLGLVTNLGIGSMQVSSGLENLFGMEHSNTNLLIVIIVMSTVATIAA 253 Query: 307 VRGIDGGVKLLSNVNMIVAFALLIFIT-FITFDTAMGSLVDTTMAYIQNII----PLSNP 361 V G++ G++ LSN+N+++ LLIF+ F + LV T Y+ II L Sbjct: 254 VSGVENGIRRLSNLNIVLFSGLLIFVLLFGPTLHLLNGLVQNTGDYLNGIILKTFDLYVY 313 Query: 362 HGREDET--WMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVTLVW 419 G D+T WM WT+FYWAWW+SW+PFVGMFIAR+S+GRTVRE + V++IP TL W Sbjct: 314 EGDADKTERWMGLWTLFYWAWWISWAPFVGMFIARISRGRTVRELVAGVLLIPLGFTLAW 373 Query: 420 MSVFGGIALDQVVNK-VGELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFITS 478 +S+FG ALD V+N+ LG L S+ ++ + + P S ++ +SI + V F+T Sbjct: 374 LSIFGNSALDLVLNQGAVALGKTALEQPSMAIYQLLEHYPASKIVIGVSIFVGFVLFLTP 433 Query: 479 SDSGSLVIDSITA-GGKIDAPVPQ--RIFWACIEGSIAAVMLWVGGKEALQALQSGVVAT 535 +DSG++++ +++ GG +D P RIFW+ + + +L+ G EA+Q + VV Sbjct: 434 ADSGAVMMANLSCKGGNVDEDAPHWLRIFWSAVITLVTIGLLFAGNFEAMQTM---VVLA 490 Query: 536 GLPFTFVLLLMCVSLVKGLRTELS 559 GLPF+ VL+ L K +R +++ Sbjct: 491 GLPFSVVLIFFMFGLHKAMRQDVA 514 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: 974 Number of extensions: 52 Number of successful extensions: 7 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: 663 Length adjustment: 37 Effective length of query: 525 Effective length of database: 626 Effective search space: 328650 Effective search space used: 328650 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: 53 (25.0 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