Align citrate transporter (characterized)
to candidate BWI76_RS08245 BWI76_RS08245 MFS transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__Koxy:BWI76_RS08245 Length = 431 Score = 793 bits (2049), Expect = 0.0 Identities = 395/428 (92%), Positives = 413/428 (96%) Query: 1 MTQQPSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFG 60 MTQ SRAGT GAILRVTSGNFLEQFDFFLFGFYATYIA+TFFPAESEFAALMLTFAVFG Sbjct: 1 MTQPSSRAGTIGAILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFAALMLTFAVFG 60 Query: 61 SGFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVG 120 SGFLMRPIGA+VLGAYIDRIGRRKGLM+TLAIMGCGTLLIALVPGYQTIG+LAP+LV+VG Sbjct: 61 SGFLMRPIGAIVLGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGILAPILVVVG 120 Query: 121 RLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHD 180 RLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGY LN TLGHD Sbjct: 121 RLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYALNETLGHD 180 Query: 181 EISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAG 240 +I+EWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREI +TI KNWRII+AG Sbjct: 181 QIAEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREILSTIVKNWRIISAG 240 Query: 241 TLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGR 300 TLLVAMTTTTFYFITVYTPTYGR VL+LSARDSL+VTMLVGISNFIWLPIGGAISD+IGR Sbjct: 241 TLLVAMTTTTFYFITVYTPTYGRAVLHLSARDSLLVTMLVGISNFIWLPIGGAISDKIGR 300 Query: 301 RPVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVY 360 RPVLMGITLLAL+TT PVM+WLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVY Sbjct: 301 RPVLMGITLLALLTTWPVMHWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVY 360 Query: 361 VRTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLFARL 420 VRTVGFSLAFSLATAIFGGLTPAISTALV++TGDKSSPGWWLMCAALCG AAT MLF RL Sbjct: 361 VRTVGFSLAFSLATAIFGGLTPAISTALVEITGDKSSPGWWLMCAALCGFAATAMLFVRL 420 Query: 421 SSGYQTVE 428 S GY+ E Sbjct: 421 SRGYRPAE 428 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: 765 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: 431 Length adjustment: 32 Effective length of query: 399 Effective length of database: 399 Effective search space: 159201 Effective search space used: 159201 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