Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate WP_012970608.1 ALVIN_RS06905 high-affinity choline transporter BetT
Query= SwissProt::Q87NZ5 (553 letters) >NCBI__GCF_000025485.1:WP_012970608.1 Length = 669 Score = 462 bits (1190), Expect = e-134 Identities = 227/499 (45%), Positives = 332/499 (66%), Gaps = 22/499 (4%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF IS +++FV+ + EP F G+++W++ + WF++ S F++ VL T Sbjct: 26 VFIISAALVLIFVLFAALATEIAEPLFKGMQSWVIESAGWFYVLSVAGFLVFVAVLAFTS 85 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 LGR+++G + PDY YA WLAMLF+AGMGIGL+FFGV+EP+ HF+S Sbjct: 86 LGRIKLGPEHSQPDYGYASWLAMLFSAGMGIGLMFFGVAEPVMHFASP------------ 133 Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224 P+G G A A M T +HW +H W+IYA++AL LA F+F LPL++RS Y Sbjct: 134 ---PVGDPQGIEAARQA--MRITFFHWGIHAWAIYAVVALSLAYFAFRHDLPLSIRSALY 188 Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIV 284 PL GER++G +GH +DI AVV T+FG+ATSLG+G Q +GLN+LF +P+ TTQVVLI Sbjct: 189 PLIGERIYGPIGHAVDIFAVVGTLFGVATSLGFGVIQINSGLNYLFDIPVGITTQVVLIA 248 Query: 285 VITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNI 344 VITA+A +SVV GLD+G++RLSE+NMILA LL FV++ GPT+ +L N Y++++ Sbjct: 249 VITAIATLSVVLGLDAGIRRLSELNMILAVALLAFVLVAGPTVFLLQTLVQNTGMYLSSL 308 Query: 345 PALSMP-FEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPST 403 ++ + E ++ GWT FYW WWI+W+PFVG+FIARVSRGR++REF++ V+ +P+ Sbjct: 309 FEMTFNLYAYEPNDWIGGWTLFYWGWWIAWAPFVGLFIARVSRGRTIREFVLGVLFVPTG 368 Query: 404 VCVLWMTAFGGTAISQYVNDGYEAVFN---AELPLKLFAMLDVMPFAEITSVVGIILVVV 460 +WMT FG TAI + G + + A+ + LF + +P + IT+V+ +L+V Sbjct: 369 FTFMWMTFFGDTAIHMILMQGIGELADAVAADTSVALFKFFEYLPLSNITAVLATLLIVT 428 Query: 461 FFITSSDSGSLVIDTI-AAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAMAVTT 519 FF+TSSDSGSLV+D + + GG+ ++P QR+FW EG+VA AL++ GGL+A Q + + Sbjct: 429 FFVTSSDSGSLVVDMLTSGGGQTESPVWQRIFWAAVEGVVAAALLIAGGLSALQTATIAS 488 Query: 520 GLPFTIVLLVATVSLIKGL 538 LPFTIV+++ L++ L Sbjct: 489 ALPFTIVMILMCWGLMRAL 507 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: 1022 Number of extensions: 61 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: 669 Length adjustment: 37 Effective length of query: 516 Effective length of database: 632 Effective search space: 326112 Effective search space used: 326112 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: 53 (25.0 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