Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate 14452 b0314 choline transporter of high affinity (NCBI)
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__Keio:14452 Length = 677 Score = 340 bits (872), Expect = 1e-97 Identities = 179/507 (35%), Positives = 289/507 (57%), Gaps = 30/507 (5%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF S I+LF + T+ FR + W+ W++L + ++++ + + + Sbjct: 17 VFYTSAGLILLFSLTTILFRDFSALWIGRTLDWVSKTFGWYYLLAATLYIVFVVCIACSR 76 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 G V++G ++ P++S W AMLFAAG+GI L+FF V+EP++ + Sbjct: 77 FGSVKLGPEQSKPEFSLLSWAAMLFAAGIGIDLMFFSVAEPVTQYMQ------------- 123 Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224 P GA G T A+ M T++H+ L WS+YAL+ + L FS+ LPLT+RS Y Sbjct: 124 ---PPEGA-GQTIEAARQAMVWTLFHYGLTGWSMYALMGMALGYFSYRYNLPLTIRSALY 179 Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIV 284 P+FG+R+ G +GH +DI AV+ T+FG+AT+LG G Q GL+ LF +P + + LI Sbjct: 180 PIFGKRINGPIGHSVDIAAVIGTIFGIATTLGIGVVQLNYGLSVLFDIPDSMAAKAALIA 239 Query: 285 VITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNI 344 + +A ISV +G+D G++ LSE+N+ LA L+ FV+ +G T +L N+ Y+ Sbjct: 240 LSVIIATISVTSGVDKGIRVLSELNVALALGLILFVLFMGDTSFLLNALVLNVGDYVNRF 299 Query: 345 PAL---SMPFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIP 401 + S F+R V + WT F+WAWW++WSPFVG+F+AR+SRGR++R+F++ ++IP Sbjct: 300 MGMTLNSFAFDR-PVEWMNNWTLFFWAWWVAWSPFVGLFLARISRGRTIRQFVLGTLIIP 358 Query: 402 STVCVLWMTAFGGTAISQYVNDGYEAVFNAELPLK----LFAMLDVMPFAEITSVVGIIL 457 T +LW++ FG +A+ + ++ G A F E + +++L P ++ V I Sbjct: 359 FTFTLLWLSVFGNSALYEIIHGG--AAFAEEAMVHPERGFYSLLAQYPAFTFSASVATIT 416 Query: 458 VVVFFITSSDSGSLVIDTIAAGGK---VDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQA 514 ++F++TS+DSG+LV+ + K DAP RVFW GL+ + +++ G++A Q Sbjct: 417 GLLFYVTSADSGALVLGNFTSQLKDINSDAPGWLRVFWSVAIGLLTLGMLMTNGISALQN 476 Query: 515 MAVTTGLPFTIVLLVATVSLIKGLMDE 541 V GLPF+ V+ L K L E Sbjct: 477 TTVIMGLPFSFVIFFVMAGLYKSLKVE 503 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: 937 Number of extensions: 58 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: 677 Length adjustment: 37 Effective length of query: 516 Effective length of database: 640 Effective search space: 330240 Effective search space used: 330240 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 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