Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate WP_019894743.1 A377_RS0103365 high-affinity choline transporter BetT
Query= SwissProt::Q87NZ5 (553 letters) >NCBI__GCF_000384235.1:WP_019894743.1 Length = 661 Score = 441 bits (1134), Expect = e-128 Identities = 217/497 (43%), Positives = 320/497 (64%), Gaps = 22/497 (4%) Query: 46 FAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTPL 105 + SG+ I+L A E F GL++ ++SN WF++ + + +I L ++ Sbjct: 20 YTASGLVILLLAYAA-AMPTHAEATFNGLQSVIISNFGWFYVLTVAIVLITVAFLGLSRY 78 Query: 106 GRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRTD 165 G +++G A+PDY+ W +MLF+AGMGIGL+FFGV+EP+ H+ S Sbjct: 79 GDIKLGPDHASPDYTKITWFSMLFSAGMGIGLMFFGVAEPVMHYLS-------------- 124 Query: 166 WAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFYP 225 P G +AA M T +HW LH W+IYA++AL LA FS+ GLPLT+RS YP Sbjct: 125 --PPVAESGTVEAARE-AMRITFFHWGLHAWAIYAIVALILAFFSYRHGLPLTLRSALYP 181 Query: 226 LFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIVV 285 GE+++G +GH +DI AV+ T+FG+ATSLGYG Q +GLN LF +P+ TQ++LI Sbjct: 182 FIGEKIYGPIGHAVDIFAVIGTIFGIATSLGYGVLQMNSGLNTLFDIPIGVVTQIILIAA 241 Query: 286 ITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNIP 345 +T LA ISV GLD G++RLSE+NM LA +L+F V+ +G T+ ++ N +Y+++I Sbjct: 242 VTGLAAISVATGLDKGIRRLSELNMSLAIILMFMVLFLGSTVFLMQALIQNAGTYMSDII 301 Query: 346 ALSMP-FEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPSTV 404 ++ F E ++ GWT FYWAWW++W+PFVG+FIARVSRGRS+REF+ V+ +P Sbjct: 302 RVTFNLFAYEKTDWIGGWTIFYWAWWLAWAPFVGLFIARVSRGRSIREFVTGVLFVPVGF 361 Query: 405 CVLWMTAFGGTAISQYVNDGYEAVFNA---ELPLKLFAMLDVMPFAEITSVVGIILVVVF 461 ++W T FG +AI +NDG ++ +A ++ + LFA LD PF + S + I++VV+F Sbjct: 362 SMMWFTFFGNSAIDMILNDGLSSLGDAVSNDVAVALFAFLDQFPFGSVLSFIAIVMVVIF 421 Query: 462 FITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAMAVTTGL 521 F+TS+DSG+LV++ + + G+ D P QR++W GL+AI L+L GGL A Q M + + L Sbjct: 422 FVTSADSGALVVNMLCSNGRDDTPLWQRMYWVIGIGLIAIILLLAGGLGALQTMTIASAL 481 Query: 522 PFTIVLLVATVSLIKGL 538 PF+IVLL+AT LIK L Sbjct: 482 PFSIVLLIATYGLIKAL 498 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: 996 Number of extensions: 52 Number of successful extensions: 5 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: 661 Length adjustment: 37 Effective length of query: 516 Effective length of database: 624 Effective search space: 321984 Effective search space used: 321984 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