Align citrate transporter (characterized)
to candidate BPHYT_RS15025 BPHYT_RS15025 major facilitator transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__BFirm:BPHYT_RS15025 Length = 433 Score = 532 bits (1371), Expect = e-156 Identities = 260/416 (62%), Positives = 323/416 (77%), Gaps = 4/416 (0%) Query: 2 TQQPSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGS 61 T Q S+ T + RV SGNFLE +DF ++G+YA+ IAKT+FP+ +EFA+LML+ +VFG+ Sbjct: 10 TSQESKVKT---VFRVVSGNFLEMYDFMVYGYYASAIAKTYFPSGNEFASLMLSLSVFGA 66 Query: 62 GFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGR 121 GFLMRP+GA+VLGAYID GRRKGL++TL +M GTL +A +PGY TIGLLAPVLVL GR Sbjct: 67 GFLMRPLGAIVLGAYIDHHGRRKGLILTLGLMALGTLTVASIPGYATIGLLAPVLVLGGR 126 Query: 122 LLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDE 181 LLQGFSAGVELGGVSVYLSEIAT GNKGFY +WQS SQQVA+V AALIG LN L D+ Sbjct: 127 LLQGFSAGVELGGVSVYLSEIATKGNKGFYCAWQSGSQQVAVVFAALIGVFLNKLLPADQ 186 Query: 182 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGT 241 ++ WGWR+PF IGC+I+P +F++RRSLQETE F RKH P EI T+A NW I+ G Sbjct: 187 MTAWGWRVPFLIGCLIVPFLFLIRRSLQETEEFKARKHHPKMGEIMKTMAANWGIVLGGM 246 Query: 242 LLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRR 301 +V MTT +FY IT YTPT+G+ VL LS+ D+L+VT+ +G+SN +WLP+ GA+SDRIGRR Sbjct: 247 GMVIMTTVSFYMITAYTPTFGKEVLKLSSIDTLIVTVCIGLSNLVWLPLAGALSDRIGRR 306 Query: 302 PVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYV 361 PVL+ T+L ++T P + WL A P F R+ V LW SF +G YNG MV ALTEVMPV V Sbjct: 307 PVLLAFTILTILTAYPALQWLVADPSFARLLEVELWLSFLYGSYNGGMVVALTEVMPVEV 366 Query: 362 RTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLF 417 RT GFSLA+SLAT I GG TPAIST L+ TG+K++PG +L AA+CGL AT +L+ Sbjct: 367 RTAGFSLAYSLATTI-GGFTPAISTLLIHSTGNKAAPGLFLGAAAICGLIATLVLY 421 Lambda K H 0.328 0.141 0.432 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: 577 Number of extensions: 23 Number of successful extensions: 3 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: 431 Length of database: 433 Length adjustment: 32 Effective length of query: 399 Effective length of database: 401 Effective search space: 159999 Effective search space used: 159999 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 (21.8 bits) S2: 51 (24.3 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