Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_057687578.1 ABB28_RS17180 high-affinity choline transporter BetT
Query= SwissProt::G3XCN6 (706 letters) >NCBI__GCF_001431535.1:WP_057687578.1 Length = 659 Score = 511 bits (1317), Expect = e-149 Identities = 270/647 (41%), Positives = 395/647 (61%), Gaps = 18/647 (2%) Query: 56 PVF-VGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAF 114 PVF V SV V+A V + + P A + Q S GW YLL++ ++L ++ A Sbjct: 16 PVFAVASVIVVAFAVFVSLF-PLGAGRMLMQAQDWASSNVGWYYLLAMTLYLVFVVVAAL 74 Query: 115 SRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLT-IA 173 S YG +KLG D EPEF YLSW MLFAAG+ I L +F V EP+THF PP+ +P A Sbjct: 75 SPYGSIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHFMQPPQGDPAAGEA 134 Query: 174 AQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHV 233 R+AM + F HWG+H W ++++ +++AYF YR+NLPL +RS LYPL+ I+GPIG+ Sbjct: 135 GARQAMQLLFLHWGLHGWGVFALAAMAMAYFAYRHNLPLALRSALYPLIGNRINGPIGYT 194 Query: 234 VDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGV 293 VD I T+FGL +GFG+L +N+GL +L +P + VQ+ L+ ++ A VTGV Sbjct: 195 VDALGIVATVFGLGADMGFGVLHLNAGLAHLFDVPHTHGVQITLIVLMMGAAVAVAVTGV 254 Query: 294 EKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRP 353 EKGVR +S N+ LA+ L+LF+L GPT L+ +QN G YL S+V ++F++YAY +P Sbjct: 255 EKGVRWMSNINMLLAIALVLFMLFAGPTQYLLGTLMQNAGDYLGSVVGKSFDVYAYGGKP 314 Query: 354 -WIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTA 412 W+ SWT+FYWAWWI WSPFVG+FIARISRGRT+R+FV VL +P FT W+++FGN+A Sbjct: 315 GWMGSWTVFYWAWWIGWSPFVGLFIARISRGRTIRQFVFGVLLIPLGFTLAWLSIFGNSA 374 Query: 413 IYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVI 472 + +LA+ D L+ E PW + VL+ +FFVTS+DSG++V+ Sbjct: 375 LDQVLHHGQSQLAQLAIDDPPTVLYALLESYPWSRAVIAVTVLVSFVFFVTSADSGAVVL 434 Query: 473 DTIASGG---ETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLIL 529 T++S G E P R+FW +++ +V A LL G + AL+SA + +LPFS V+L++ Sbjct: 435 STLSSHGGAPEDDGPRWLRVFWGTVTAVVTAGLLLAGNMDALKSAVVLASLPFSAVLLLM 494 Query: 530 VWSLFVGMRADLARTQSPGSLGPRAYPASGVP-----WQRRLAMTLSTPDRRAVEKFLQA 584 W L MR+ + +L RA P G W++RL ++ P R V +F+ A Sbjct: 495 AWGL---MRSFADESHRKRALQYRASPLVGASRHHQGWRQRLGQAVNFPVRDQVYRFMDA 551 Query: 585 SVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAY 644 V PA+EAVA +L R V E G + L+V +DF+Y V ++ +++P+F ++ Sbjct: 552 DVKPAMEAVAEQL--RGDGWEVSTRLEAGDMELSVNHGDQQDFLYRVILTGYRVPSFASH 609 Query: 645 DATVADVRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691 A + Y A +GS+ YD++ + QIIND++ Q+ER+ F+ Sbjct: 610 QARNSRY-YRAEVHLYEGSQDYDLVDYSREQIINDIISQYERHVQFL 655 Lambda K H 0.326 0.139 0.422 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: 1141 Number of extensions: 69 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: 706 Length of database: 659 Length adjustment: 39 Effective length of query: 667 Effective length of database: 620 Effective search space: 413540 Effective search space used: 413540 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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