Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_082908457.1 BJL86_RS11120 BCCT family transporter
Query= SwissProt::Q87PP5 (562 letters) >NCBI__GCF_001659785.1:WP_082908457.1 Length = 597 Score = 318 bits (815), Expect = 4e-91 Identities = 181/474 (38%), Positives = 281/474 (59%), Gaps = 36/474 (7%) Query: 108 DAFFMWSTN-----FFLL------FAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAA 156 D+ F W+T F L+ F + L S G IR+G P++ T SW++M+FAA Sbjct: 78 DSAFSWTTGNLGWAFVLIQTSAVGFVIYLALSKYGAIRIGADGERPEYRTGSWIAMMFAA 137 Query: 157 GMGIGLLFWSVAEPTAYFTDWWGTPLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVAL 216 GMGIGL+F+ V+EP A+F D +A+ T FHWG+H WS YA+V L Sbjct: 138 GMGIGLMFFGVSEPLAHFHD------APPGVDEPTYGMALATTAFHWGMHPWSGYAVVGL 191 Query: 217 ALAFFAFNKGLPLSLRAAFYPIFGDR-AWGWLGHVIDILAVLSTLFGLATSLGLGAQQAT 275 ALA A+ G + A P+ G++ A G LG +D+L +L+T+FG A SLGLGA Q Sbjct: 192 ALALTAYRYGRTHLISQAMIPVIGEKNAKGGLGKFLDVLTILATIFGTACSLGLGALQIQ 251 Query: 276 SGINHVFGLNG-GIGTQMVVIAFVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITF 334 +G+N ++ GIG + VI + ++S G+ G++LLSN+NM++A L +F+ Sbjct: 252 TGLNETGAISTTGIGIVIGVIVVLGLAFLVSAASGVSKGIQLLSNINMVLALCLALFVAI 311 Query: 335 ITFDTAMG-SLVDTTMA-YIQNIIPLSNPHGR----EDETWMHGWTVFYWAWWVSWSPFV 388 + + +L+ T++ Y+QN + +++ G E W+ WT+FYWAWWVSWSPFV Sbjct: 312 FSGALVLILNLIPTSLGQYLQNFLDMASRTGASQNGEAGEWLGSWTIFYWAWWVSWSPFV 371 Query: 389 GMFIARVSKGRTVREFLFAVIVIPTLVTLVWMSVFGGIALDQVVNKVGELGANGLTDISL 448 GMF+AR+S+GRT+R+F+ V+++P +++VW S+FGG AL + +G+ + D + Sbjct: 372 GMFLARISRGRTIRQFVAGVVLVPAGMSIVWFSIFGGTALH--LEAIGDT----IRDAEV 425 Query: 449 T---LFHVYDVLPYSSVISILSIVLILVFFITSSDSGSLVIDSITAGGKIDAPVPQRIFW 505 + LF+V LP S++I IL++ LI +FFITS+DS S+V+ + G + +F+ Sbjct: 426 SERELFNVASNLPGSTIIMILAMALIAIFFITSADSASVVMGGMGQYGIEEPARYVTVFF 485 Query: 506 ACIEGSIAAVMLWV--GGKEALQALQSGVVATGLPFTFVLLLMCVSLVKGLRTE 557 G+IA +ML GG EAL +LQS + PF +L+++ VS++K LR + Sbjct: 486 GICTGAIAIIMLLAGGGGSEALDSLQSITIIAASPFLIILVVLAVSIMKMLRAD 539 Lambda K H 0.327 0.141 0.445 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: 913 Number of extensions: 50 Number of successful extensions: 8 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: 562 Length of database: 597 Length adjustment: 36 Effective length of query: 526 Effective length of database: 561 Effective search space: 295086 Effective search space used: 295086 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