Align Ectoine/glycine betaine/proline transporter EctP (characterized)
to candidate BWI76_RS07630 BWI76_RS07630 high-affinity choline transporter BetT
Query= SwissProt::Q79VE0 (615 letters) >FitnessBrowser__Koxy:BWI76_RS07630 Length = 677 Score = 341 bits (874), Expect = 7e-98 Identities = 175/497 (35%), Positives = 280/497 (56%), Gaps = 12/497 (2%) Query: 20 KSDPFIFSISVGFIVVFVIATIALGEKARTTFSAIAGWLLENLGWMYIGGVSLVFIFLMG 79 K +P +F S G I++F + T+ + + W+ GW Y+ +L +F++ Sbjct: 12 KINPVVFYTSAGLILLFSLMTLFFSDFSAAWIGRTLNWVSRTFGWYYLLAATLYIVFVVC 71 Query: 80 IFASRYGRVKLGDDDDDPEHTLIVWFCMLFAGGVGAVLMFWGVAEPINHAFNVPMANEES 139 I SR+G VKLG + PE +++ W MLFA G+G LMF+ VAEP+ P ++ Sbjct: 72 IACSRFGSVKLGPEHSKPEFSVLSWAAMLFAAGIGIDLMFFSVAEPVTQYMQPPEGAGQT 131 Query: 140 MSEAAIVQAFAYTFYHFGIHMWVIMALPGLSLGYFIYKRKLPPRLSSVFSPILGKHIYST 199 M A QA +T +H+G+ W + AL G++LGYF Y+ LP + S PI GK I Sbjct: 132 MEAAR--QAMVWTLFHYGLTGWSMYALMGMALGYFSYRYNLPLTIRSALYPIFGKKINGP 189 Query: 200 PGKLIDVLAIVGTTFGIAVSVGLGVLQINAGMNKLWSTPQVSWVQLLIILIITAVACISV 259 G +D+ A++GT FGIA ++G+GV+Q+N G++ L++ P + +I++ +A ISV Sbjct: 190 IGHSVDIAAVIGTIFGIATTLGIGVVQLNYGLSVLFNIPDSLGAKAALIVLSVIIATISV 249 Query: 260 ASGLDKGIKLLSNINIAMAVALMFFILFTGPTLTLLRFLVESFGIYASWMPNLMFWTDSF 319 SG+DKGI++LS +N+ +A+ L+ FILF G T LL LV + G Y + + + +F Sbjct: 250 TSGVDKGIRILSELNVVLALGLILFILFMGDTEFLLNALVLNVGDYVNRFMGMTLNSFAF 309 Query: 320 QDNPGWQGKWTVFYWAWTICWSPYVGMFVARISRGRTVREFIGGVLALPAIFGVVWFSIF 379 W WT+F+WAW + WSP+VG+F+ARISRGRT+R+F+ G L +P F ++W S+F Sbjct: 310 DRPVEWMNNWTLFFWAWWVAWSPFVGLFLARISRGRTIRQFVVGTLIIPFTFTLLWLSVF 369 Query: 380 GRAGI-EVELSNPGFLTQPTVVEGDVPAALFNVLQEYPLTGIVSAFALVIIVIFFITSID 438 G + + E+ N F + +N+L +YP ++ A + ++F++TS D Sbjct: 370 GNSALYEIIHGNAAFAAEAV---AHPERGFYNLLAQYPAFTFSASVATITGLLFYVTSAD 426 Query: 439 SAALVNDMFAT---GAENQTPTSYRVMWACTIGAVAGSLLIISPSSGIATLQEVVIIVAF 495 S ALV F + + P R+ W+ IG + +L+ ++GI+ LQ +I+ Sbjct: 427 SGALVLGNFTSKLKDINSDAPNWLRIFWSVVIGLLTLGMLM---TNGISALQNATVIMGL 483 Query: 496 PFFLVQFVMMFSLLKGM 512 PF V F +M L K + Sbjct: 484 PFSFVIFFVMAGLYKSL 500 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: 1055 Number of extensions: 59 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: 615 Length of database: 677 Length adjustment: 38 Effective length of query: 577 Effective length of database: 639 Effective search space: 368703 Effective search space used: 368703 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 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