Align citrate transporter (characterized)
to candidate BPHYT_RS27915 BPHYT_RS27915 major facilitator transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__BFirm:BPHYT_RS27915 Length = 439 Score = 615 bits (1585), Expect = e-180 Identities = 295/421 (70%), Positives = 351/421 (83%) Query: 2 TQQPSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGS 61 T SR+ A+LRVTSGNFLEQFDFFLFGFYAT+I+K FFP+ SEFA+LMLTFAVFG+ Sbjct: 10 TSSVSRSTRAAAVLRVTSGNFLEQFDFFLFGFYATFISKIFFPSTSEFASLMLTFAVFGA 69 Query: 62 GFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGR 121 GFLMRP+GA+ LGAYID++GRR GL++TL+IM GT+LIA VPGY +IGLLAP LVL+GR Sbjct: 70 GFLMRPLGAIFLGAYIDKVGRRMGLIVTLSIMASGTVLIACVPGYASIGLLAPALVLLGR 129 Query: 122 LLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDE 181 LLQGFSAG ELGGVSVYL+E+ATPGN+GFYTSWQSASQQVAIV+AA IGYGLN L + Sbjct: 130 LLQGFSAGAELGGVSVYLAEMATPGNRGFYTSWQSASQQVAIVMAAAIGYGLNEWLSAQQ 189 Query: 182 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGT 241 I WGWR+PF IGC I+P +F+LRRSLQET AF R+H P REIF+ + NWRI+ G Sbjct: 190 IGAWGWRVPFLIGCAIVPFLFMLRRSLQETAAFEARQHHPQAREIFSMLLANWRIVIGGM 249 Query: 242 LLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRR 301 LL AMTTTTFY ITVYTPT+GR+VL LS DSL+VT+LV +SNF+WLPIGGA+SDRIGR+ Sbjct: 250 LLTAMTTTTFYLITVYTPTFGRSVLKLSTADSLMVTLLVAVSNFVWLPIGGAVSDRIGRK 309 Query: 302 PVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYV 361 P+L+ +++LA+ T P ++WL AP F RM +VLLWFSFFFGMYNGAMVAALTEVMP V Sbjct: 310 PLLLAVSVLAIFTAYPALSWLADAPSFARMLIVLLWFSFFFGMYNGAMVAALTEVMPAEV 369 Query: 362 RTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLFARLS 421 R GFSLAFSLATA+FGG TPA+ST L+Q+T DK++PG+WL AALCGL AT L+ R + Sbjct: 370 RVAGFSLAFSLATAVFGGFTPAVSTYLIQVTHDKAAPGYWLSFAALCGLCATLGLYRRRA 429 Query: 422 S 422 S Sbjct: 430 S 430 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: 639 Number of extensions: 32 Number of successful extensions: 2 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: 439 Length adjustment: 32 Effective length of query: 399 Effective length of database: 407 Effective search space: 162393 Effective search space used: 162393 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