Align citrate transporter (characterized)
to candidate HSERO_RS07330 HSERO_RS07330 major facilitator transporter
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__HerbieS:HSERO_RS07330 Length = 432 Score = 573 bits (1478), Expect = e-168 Identities = 270/416 (64%), Positives = 339/416 (81%) Query: 2 TQQPSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGS 61 T ++ +LRVTSGNFLE FDFFL+GFYA+YI+KTFFP+++EF +L+LTF FG+ Sbjct: 4 TTTNAKHSKLSTVLRVTSGNFLEMFDFFLYGFYASYISKTFFPSDNEFVSLILTFGTFGA 63 Query: 62 GFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGR 121 GFLMRP+GA++LG+YIDR+GRR+GL++TLAIM GTLLIA VPGY TIG+ AP+LVL GR Sbjct: 64 GFLMRPLGAIILGSYIDRVGRRQGLIVTLAIMAIGTLLIAFVPGYATIGVAAPILVLTGR 123 Query: 122 LLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDE 181 LLQGFSAGVELGGVSVYL+E+ATPGNKGFY SWQSASQQ AI+ +ALIGY ++ +L + Sbjct: 124 LLQGFSAGVELGGVSVYLAEMATPGNKGFYVSWQSASQQAAIMASALIGYLVSQSLSPVQ 183 Query: 182 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGT 241 IS+WGWRIPFFIGCMI+P IF++RRSLQET+ FL RK P EI ++IA+NW+I+ AG Sbjct: 184 ISDWGWRIPFFIGCMIVPAIFIIRRSLQETDEFLARKRHPSFGEIMSSIAQNWKIVVAGM 243 Query: 242 LLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRR 301 ++V MTT +FY ITVYTPT+G+ VL LSA DSL+VT VG+SNF WLPI GA+SDR+GRR Sbjct: 244 MMVVMTTVSFYLITVYTPTFGKNVLKLSASDSLIVTFCVGLSNFCWLPIMGALSDRVGRR 303 Query: 302 PVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYV 361 PVL+ TLL L+T PVM+WL + F + + LW SF + YNGA V ALTEVMP +V Sbjct: 304 PVLVAFTLLTLLTAYPVMSWLVSDISFKNLLITELWLSFLYASYNGAAVVALTEVMPAHV 363 Query: 362 RTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLF 417 RTVGFSLA+SLATAIFGG TP +ST L++ +GDK++PG+W+ AA+CGL AT +L+ Sbjct: 364 RTVGFSLAYSLATAIFGGFTPLVSTWLIETSGDKAAPGYWMSFAAVCGLLATLVLY 419 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: 630 Number of extensions: 23 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: 432 Length adjustment: 32 Effective length of query: 399 Effective length of database: 400 Effective search space: 159600 Effective search space used: 159600 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