Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate WP_086508196.1 BZY95_RS01280 BCCT family transporter
Query= SwissProt::Q87NZ5 (553 letters) >NCBI__GCF_002151265.1:WP_086508196.1 Length = 527 Score = 384 bits (987), Expect = e-111 Identities = 205/512 (40%), Positives = 306/512 (59%), Gaps = 28/512 (5%) Query: 38 GLDIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVC 97 G+ +H VF S I+ V + +++E ++ + NL WF+L + N F+I+ Sbjct: 20 GVPVHRAVFLSSATLILALVAFGVAMPERLEAGAEAVQDAISHNLGWFYLLAMNAFLILA 79 Query: 98 LVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVN 157 L LI + G VR+GG + P++S GW +MLFAAG G+GL+F+GV+EP+S F+ Sbjct: 80 LYLIFSRYGSVRLGGEDERPEFSNWGWFSMLFAAGTGVGLLFYGVAEPVSFFADP----- 134 Query: 158 IENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPL 217 P G A +T+ A++ + + +HW LH WS+Y L+ L L F +N+GLPL Sbjct: 135 ----------PFGEA--ETEQAASDALVHSYFHWGLHGWSMYGLVGLALCYFCYNRGLPL 182 Query: 218 TMRSIFYPLFGE-RVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTD 276 T+RS F PL G+ RV G +G+ ID +A T+ G+A SLG G Q TGL +G+P Sbjct: 183 TIRSAFMPLLGKKRVEGPIGNGIDAMAATGTLIGVAVSLGLGVRQINTGLEHAYGIPDNI 242 Query: 277 TTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDN 336 Q+ LI IT +ALISV++GL G+++LS++ +++ A L+ +V++ GPT I + Sbjct: 243 GVQIALIAGITTVALISVLSGLAKGIQQLSKLALLIGAALVLYVLLFGPTQFIFNSMLQS 302 Query: 337 IASYITNIPA---LSMPFEREDV-NYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVRE 392 +YI IP+ + F D ++ WT FY+AWWISWSPFVG+FIARVSRGR++R+ Sbjct: 303 FGNYINEIPSRGTFTEAFNPPDAESWQSEWTLFYFAWWISWSPFVGLFIARVSRGRTLRQ 362 Query: 393 FIICVILIPSTVCVLWMTAFGGTAISQYVND--GYEAVFNAELPLKLFAMLDVMPFAE-- 448 +++ V+L+P+ VLW+T GG+A+ + + + G + E L F LD E Sbjct: 363 YLLGVLLVPTLTSVLWLTVMGGSALYRELFEAAGLVDIVEDEPELAFFLFLDHFHMPEWI 422 Query: 449 --ITSVVGIILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLG 506 + + I+ V +FFITSSDSGSL+ID I +GG P R+FW EG+VA+ L+ Sbjct: 423 VTTSMTLMIVTVAIFFITSSDSGSLIIDIITSGGDPHPPRTTRMFWAIMEGVVAVILLTA 482 Query: 507 GGLAAAQAMAVTTGLPFTIVLLVATVSLIKGL 538 GGL A QA+A +GLPF ++LL+ L GL Sbjct: 483 GGLEALQAVATISGLPFVVILLLMCTGLYLGL 514 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: 801 Number of extensions: 43 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: 527 Length adjustment: 35 Effective length of query: 518 Effective length of database: 492 Effective search space: 254856 Effective search space used: 254856 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 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