Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_090271580.1 BLU11_RS00755 BCCT family transporter
Query= SwissProt::Q87PP5 (562 letters) >NCBI__GCF_900105005.1:WP_090271580.1 Length = 685 Score = 389 bits (998), Expect = e-112 Identities = 203/501 (40%), Positives = 312/501 (62%), Gaps = 11/501 (2%) Query: 61 WGFDIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLL 120 W I PVF I + + L+ +P A + + + + I F F+M S FL+ Sbjct: 10 WNTTILLPVF-IPSFFFILLLVISTATQPELAGELFSSVLSYITTTFGWFYMLSVAIFLV 68 Query: 121 FAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGT 180 F V + S G I+LG A P +S +W +MLF+AG GI LLF+ VAEP ++ + Sbjct: 69 FIVIVAMSKWGHIKLGPDHAEPQYSFPAWFAMLFSAGYGIALLFFGVAEPVLHYAE---P 125 Query: 181 PLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFG 240 P AE + DA AM FHWG H W+IY L L LA+F+F GLPLS+R+A YP+ G Sbjct: 126 PQGAEGLTVDAAKQAMQIAFFHWGFHIWAIYGLTGLVLAYFSFRHGLPLSIRSALYPLIG 185 Query: 241 DRAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVF-GLNGGIGTQMVVIAFVT 299 DR +G +GH +D A+L T+FG+AT+LGL Q +G+N+++ + GIG Q+ IAF+T Sbjct: 186 DRIYGPIGHAVDTFAILGTMFGIATTLGLSVAQINAGLNYLWPSIPIGIGVQVGTIAFIT 245 Query: 300 FIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFI-TFDTAMGSLVDTTMAYIQNIIPL 358 F+ + SV+ G+D G+K LS +NMIVA +L++F+ F + + + T +Y+ NI+ Sbjct: 246 FLTMGSVIAGMDKGIKNLSMLNMIVATSLMLFVFFAGPTIFILEAFLQNTGSYLNNIVER 305 Query: 359 S-NPHGREDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVTL 417 + N W+ WT+F + W ++W+PFVG+FIA++S+GRT+R+F+F V+++PT+ T Sbjct: 306 TFNLQAYSRSDWIGNWTLFIFGWTIAWAPFVGLFIAKISRGRTIRQFVFGVMLVPTIFTF 365 Query: 418 VWMSVFGGIALDQVVNK-VGELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFI 476 W SVFG AL ++N+ L D ++ LF +++ LP +++IS ++++LI +FFI Sbjct: 366 FWFSVFGDTALHLIINQGYSVLIDQVQADNAIALFKLFEQLPMTAIISTITVILITLFFI 425 Query: 477 TSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEALQALQSGVVATG 536 TS+DSG+LV+DS+ +GG + P QR FWA + G +A+V+L GG L+ALQS VA+ Sbjct: 426 TSADSGALVVDSLASGGALVTPAWQRGFWAILSGVLASVLLVAGG---LKALQSMAVASA 482 Query: 537 LPFTFVLLLMCVSLVKGLRTE 557 LPF ++L+ V + + L E Sbjct: 483 LPFAVIMLISAVGMWRALTIE 503 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: 1012 Number of extensions: 54 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: 562 Length of database: 685 Length adjustment: 37 Effective length of query: 525 Effective length of database: 648 Effective search space: 340200 Effective search space used: 340200 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