Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate 3607157 Dshi_0579 BCCT transporter (RefSeq)
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Dino:3607157 Length = 519 Score = 241 bits (614), Expect = 7e-68 Identities = 160/509 (31%), Positives = 250/509 (49%), Gaps = 35/509 (6%) Query: 34 VGPFGLDIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVF 93 + P G D +FA++G I LF L + + A+ ++ Sbjct: 10 LAPKGAD--KALFAVTGGFIALFCAYALFDIEGLSALVDTSFAFSAKYFGLYWQVLLLAT 67 Query: 94 VIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSAL 153 ++ LVL P R +GG +TP++ W AM+ + G VF+ EP++HF S Sbjct: 68 FLIGLVLCFLPGSRTLMGGL-STPEFGTFSWAAMIMCTLLAGGGVFWAAGEPIAHFLSTP 126 Query: 154 GGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIY-ALLALGLAIFSFN 212 G GD A + +A + HW W+I +L + L + ++ Sbjct: 127 -------------PVFGDLSGDVQAQAHAALAQSFLHWGFLAWAILGSLTTVMLMHYHYD 173 Query: 213 KGLPLTMRSIFYPLFGERVW-GWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFG 271 KGLPL R++ YPL G+R G +G I D ++A V G +G+ Q + GLN L G Sbjct: 174 KGLPLAPRTLLYPLLGDRALSGPIGLIADASCIIAVVAGTVGPIGFLGLQMSYGLNDLTG 233 Query: 272 VPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILT 331 +P T TQ + I+ + L +S + GL G+K LS+IN++LA +LL F+++ GPTM I Sbjct: 234 IPDTFATQAIAILALVGLYTVSAITGLAKGIKILSQINVLLAVVLLIFMLVAGPTMNIFA 293 Query: 332 GFFDNIASYITNIPALSMPFERE-----DVNYSQGWTAFYWAWWISWSPFVGMFIARVSR 386 GFF + Y T+ ++M + + D + WT F+W W++ + P + +FIAR+SR Sbjct: 294 GFFGGMQVYATHFFDMAM-YRGDAGLFGDAGWLGWWTVFFWGWFMGYGPLMAVFIARISR 352 Query: 387 GRSVREFIICVILIPSTVCVLWMTAFGGTAI-----SQYVNDGYEAVFNAELPLKLFAML 441 GRS+R+ II + + + W T GG+ I V G FN LP L A+ Sbjct: 353 GRSIRQIIITLSIAAPLITNFWFTIIGGSGIFFEIAEPGVVSGPFEGFN--LPAGLLAIT 410 Query: 442 DVMPFAEITSVVGIILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAI 501 MP I SV+ ++L + F T+SDS S VI + G + T R FW G++A+ Sbjct: 411 QAMPMGLILSVLFLVLTMCFVATTSDSMSYVISSTMTDG--EPSTAMRAFWGLAMGVMAL 468 Query: 502 ALML--GGGLAAAQAMAVTTGLPFTIVLL 528 L+ GG+ Q+ V T +P +++LL Sbjct: 469 ILISTGEGGIGKLQSFIVVTAVPVSLILL 497 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: 860 Number of extensions: 50 Number of successful extensions: 6 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: 519 Length adjustment: 35 Effective length of query: 518 Effective length of database: 484 Effective search space: 250712 Effective search space used: 250712 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