Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate 3608727 Dshi_2119 choline/carnitine/betaine transporter (RefSeq)
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Dino:3608727 Length = 524 Score = 374 bits (959), Expect = e-108 Identities = 206/523 (39%), Positives = 307/523 (58%), Gaps = 33/523 (6%) Query: 32 LKVGPF-GLDIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASG 90 ++ GPF G++ H + IS I+LFV+ L F + + R + W+++ Sbjct: 3 IRSGPFRGVNPHTSL--ISAGIILLFVLLVLAFPSRSADWIDAARTLITFYFGWWYVLLS 60 Query: 91 NVFVIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFS 150 VF++ + + + G +R+G + P YSY W AML+AAG GIG++F+ ++EPM H+S Sbjct: 61 GVFLVFLIAIAFSKYGAIRLGDADERPKYSYFTWFAMLYAAGQGIGIIFWSIAEPMFHYS 120 Query: 151 SALGGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFS 210 GG +G T AA+ + M T +HW L+ W+IY ++AL L + S Sbjct: 121 ---GGTPFADG------------SGTAAAADMAMQVTFFHWGLNAWAIYCIVALALCLVS 165 Query: 211 FNKGLPLTMRSIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLF 270 + PL +R YPLFG+RV G +G +ID++AV AT+FG+ATSLG G +Q GLN L+ Sbjct: 166 YRLKKPLGIRYTLYPLFGDRVEGPLGVVIDVVAVFATIFGIATSLGLGVTQINAGLNHLW 225 Query: 271 GVPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAIL 330 GVP+++T Q+VLI ITA+AL SV++GLD G+K LS++NM L LL F GPT +L Sbjct: 226 GVPISETVQLVLIAAITAVALCSVLSGLDRGIKWLSQVNMWLTIALLVFFFTWGPTQYLL 285 Query: 331 T-------GFFDNIASYITNIPALSMPFEREDVNYSQGWTAFYWAWWISWSPFVGMFIAR 383 +F ++ S+ I ++ R + WT FYW WWISW+PFVG+F+AR Sbjct: 286 VSLGEVTLAYFVSLFSFNVYIESVPAEATRWSDMWQGWWTTFYWGWWISWAPFVGVFVAR 345 Query: 384 VSRGRSVREFIICVILIPSTVCVLWMTAFGGTAISQYV--NDGYEAVFNAELPLKLFAML 441 VSRGR+VREFI+ V+ + S + +W+ A+GGTA+ V G +A + + LFA Sbjct: 346 VSRGRTVREFILGVVGVSSILSFVWIVAYGGTALWAEVLGPGGVSDAVSANVSMALFATF 405 Query: 442 DVMPFAEITSVVGI---ILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGL 498 D M I V G+ ILV +F+TSSDSG+LV+ TI + G R+ W TFEG+ Sbjct: 406 DAMDVGAIGLVAGVFGTILVTTYFVTSSDSGTLVVATILSEGNEHPMYRHRMIWGTFEGV 465 Query: 499 VAIALMLGGGLAA---AQAMAVTTGLPFTIVLLVATVSLIKGL 538 VA L++ GG AA Q A+ LPF++++++ ++I+ L Sbjct: 466 VAAVLLVVGGSAALSTLQTAAIIAALPFSVIMVLMCFAIIRCL 508 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: 903 Number of extensions: 51 Number of successful extensions: 5 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: 553 Length of database: 524 Length adjustment: 35 Effective length of query: 518 Effective length of database: 489 Effective search space: 253302 Effective search space used: 253302 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