Align citrate transporter (characterized)
to candidate HSERO_RS01150 HSERO_RS01150 membrane protein
Query= CharProtDB::CH_014606 (431 letters) >FitnessBrowser__HerbieS:HSERO_RS01150 Length = 433 Score = 296 bits (758), Expect = 8e-85 Identities = 150/402 (37%), Positives = 233/402 (57%), Gaps = 3/402 (0%) Query: 13 AILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVV 72 AI+ GN LE FDF ++ F+A IAK FFP ++ +L+L A FG GF MRP+G ++ Sbjct: 22 AIVATVIGNGLEWFDFTVYSFFAVIIAKLFFPTGNDLTSLLLAVATFGVGFFMRPVGGIL 81 Query: 73 LGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVEL 132 LG Y DR+GR+ L +T+ +M GT +I L P Y++IGL AP++++V RLLQGFSAG E+ Sbjct: 82 LGIYADRVGRKAALSVTILLMAVGTTMIGLAPTYESIGLFAPLIIVVARLLQGFSAGGEM 141 Query: 133 GGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFF 192 G + +L+E A + +Y+SW AS VA+++ A +G + +L ++ WGWR+PF Sbjct: 142 GSATAFLTEYAPERERAYYSSWIQASIGVAVLLGAAVGTFVTASLDAAALASWGWRLPFL 201 Query: 193 IGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNW-RIITAGTLLVAMTTTTF 251 +G +I P+ + +R L+ET FL+ K + D+ + +N+ R +A +V + T Sbjct: 202 LGIIIGPVGYYIRHHLEETPTFLEEKDKTDSP--LKEVIRNFPRETSASFSMVILWTVCT 259 Query: 252 YFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLMGITLLA 311 Y + Y PTY VL L + M+ G+ + PI G ++DRIGRRP+L G L Sbjct: 260 YVLLFYMPTYSVKVLKLPQTTGFIAGMVGGLCIMVLAPIVGRLADRIGRRPLLSGSAALI 319 Query: 312 LVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFS 371 L+ P+ ++ +AP + + + L F Y G ++AA +E+ P V + G S+A++ Sbjct: 320 LMLAYPMFAYINSAPSLSTLLIFQLVFGTLIAAYTGPILAAFSELFPAKVLSTGLSVAYN 379 Query: 372 LATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAAT 413 LA IFGG T L+ TG +P +++M AA T Sbjct: 380 LAVTIFGGFASFFITWLIAATGSTMAPAFYVMIAAAISFVGT 421 Score = 25.0 bits (53), Expect = 0.005 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 10/80 (12%) Query: 11 FGAILRVTSGNFLEQFDFFL------FGFYATY-IAKTFFPAESEFAALMLTFAVFGSGF 63 FG ++ +G L F G Y +A T F FA+ +T+ + +G Sbjct: 346 FGTLIAAYTGPILAAFSELFPAKVLSTGLSVAYNLAVTIFGG---FASFFITWLIAATGS 402 Query: 64 LMRPIGAVVLGAYIDRIGRR 83 M P V++ A I +G R Sbjct: 403 TMAPAFYVMIAAAISFVGTR 422 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: 501 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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