Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate GFF2787 HP15_2731 choline/carnitine/betaine transporter
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Marino:GFF2787 Length = 494 Score = 221 bits (563), Expect = 5e-62 Identities = 146/485 (30%), Positives = 241/485 (49%), Gaps = 26/485 (5%) Query: 53 IVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTPLGRVRIGG 112 I+LFV A++ V AW + L FF + + + ++ G RIGG Sbjct: 7 ILLFVGASIVDSGYVADLIGAGFAWTATYLGSFFQVLLLLTFFIAMGTALSRAGTARIGG 66 Query: 113 TEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRTDWAPLGGA 172 + P+ WL+M+ + G VFF EP+ HF + E G + AP Sbjct: 67 LDR-PEIGRFRWLSMIMCTLLAGGGVFFAAGEPVYHFVVTPPAFDTEAGSASAVAP---- 121 Query: 173 VGDTDAASALGMAATIYHWALHPWSIY-ALLALGLAIFSFNKGLPLTMRSIFYPLFGERV 231 MA + HW W++ +L AL L + +G PL R++ YP+FGE+V Sbjct: 122 ----------AMAQSFTHWGFLAWAVLGSLTALVLTRAHYGQGKPLQPRTLLYPVFGEKV 171 Query: 232 -WGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIVVITALA 290 G +G +ID V+A V G +G+ A+Q + GL+ LFGVP TQ+ ++VV+ + Sbjct: 172 IQGRLGGVIDAFCVIAVVAGTVGPIGFLATQMSFGLHELFGVPDGYGTQLTVLVVLAGVY 231 Query: 291 LISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNIPAL-SM 349 + S + GL G++ LS N+ILA ++ + + GPT+ + + ++ Y+T+ A+ +M Sbjct: 232 MTSAMTGLHKGIQLLSRFNVILALVIAGVIFVFGPTLFLANTYTQSMGEYVTSFFAMATM 291 Query: 350 PFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPSTVCVLWM 409 E + + WT F++AW+I ++P + +F+AR+SRGR+VRE ++ V ++ +W Sbjct: 292 TAETAPAWWMKWWTVFFFAWFIGYTPLMAVFVARISRGRTVREMVLAVAVLAPIATTIWF 351 Query: 410 TAFGGTAISQYVN---DGYEAVFNAELPLKLFAMLDVMPFAEITSVVGIILVVVFFITSS 466 T GG+ I + D EA+ N + + +P + ++L +F T+ Sbjct: 352 TLLGGSGIYHQLAGTFDLTEALNNFRFDVATLTVAQALPGGTWMAAAILLLTTIFVATTG 411 Query: 467 DSGSLVIDTIAAGGKVDAPTPQ-RVFWCTFEGLV-AIALMLGGG-LAAAQAMAVTTGLPF 523 DS S I + AG D P P RVFW L+ AI L +G G + Q V T +P Sbjct: 412 DSMSYSIAMVGAGH--DEPNPWIRVFWGGAMALMAAILLYMGAGQIGVLQQFIVLTAIPV 469 Query: 524 TIVLL 528 ++++L Sbjct: 470 SLIIL 474 Lambda K H 0.327 0.141 0.435 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: 744 Number of extensions: 47 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 553 Length of database: 494 Length adjustment: 35 Effective length of query: 518 Effective length of database: 459 Effective search space: 237762 Effective search space used: 237762 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