Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate PP_3628 PP_3628 Choline/carnitine/betaine transporter family protein
Query= SwissProt::Q87PP5 (562 letters) >FitnessBrowser__Putida:PP_3628 Length = 581 Score = 349 bits (896), Expect = e-100 Identities = 187/503 (37%), Positives = 307/503 (61%), Gaps = 22/503 (4%) Query: 69 VFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFAVGLLFS 128 VFG ++ L + ++ L + A A + ++ +I F FF+ +++ F++F + L S Sbjct: 37 VFGFTSLLAIAFVLWGFLNQASLASSA-SSAQSWVILNFGWFFVLTSSLFVVFVLWLAAS 95 Query: 129 PLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTPLNAEAYS 188 G++ LG P+ TVSW++M+F+AGMGIGL+F+ VAEP +++ P +A + Sbjct: 96 RYGRVPLGRDGEQPEFRTVSWVAMMFSAGMGIGLMFFGVAEPLSHYIS--PPPGSASGQT 153 Query: 189 ADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFGDRAWGWLG 248 ++A +AM T+FHW +H W++YA+V L +A+ F +G + AAF P+ G A G LG Sbjct: 154 SEAMQVAMATTLFHWTLHPWAMYAIVGLVIAYGTFRRGRSQLISAAFRPLIGKHANGPLG 213 Query: 249 HVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGGIGTQ-----MVVIAFVTFIAV 303 +ID++A+ +TLFG A SLGLGA Q G+ + NG I + + +I +T V Sbjct: 214 RLIDMMAIFATLFGSAASLGLGALQIAGGLEY----NGWIESPGKLFYISIITLLTIAFV 269 Query: 304 LSVVRGIDGGVKLLSNVNMIVAFALLIFITFITFDTAMGSLVDTTMAYIQNIIP----LS 359 S V GI G++ LSN NM++A L +F+ + M +L+ T++ ++P + Sbjct: 270 TSAVSGIGKGIQWLSNTNMVLALVLAVFVFMVGPTLLMLNLLPTSLGIYIKMLPEMMART 329 Query: 360 NPHGRED-ETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVTLV 418 N G E +W+ GWTVFYWAWW+SW+PFVGMFIAR+S+GRT+R+F+ V+++P+LV+LV Sbjct: 330 NASGGEQMNSWLAGWTVFYWAWWISWTPFVGMFIARISRGRTIRQFVTGVLLVPSLVSLV 389 Query: 419 WMSVFGGIALDQVVNKVGELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFITS 478 W ++FGG A++ V +L ANG + + L+ + D P +S S+L ++L+ +FF++ Sbjct: 390 WFTIFGGAAIEAVREGAFQL-ANGAVNSNHALYQLLDSYPLASATSVLVMILVGIFFVSG 448 Query: 479 SDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGK----EALQALQSGVVA 534 +D+ SLV+ +++ G IFW + G++AA+ML +G EAL LQ+ + Sbjct: 449 ADAASLVMGTLSEHGTTAPSRRTVIFWGTLTGTVAAIMLAIGDPGNPGEALTGLQNLTIV 508 Query: 535 TGLPFTFVLLLMCVSLVKGLRTE 557 LPF V++L+C++L + LR + Sbjct: 509 VALPFVVVMVLLCLALYRDLRKD 531 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: 883 Number of extensions: 57 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: 581 Length adjustment: 36 Effective length of query: 526 Effective length of database: 545 Effective search space: 286670 Effective search space used: 286670 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