Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate 14734 b0598 carbon starvation protein (NCBI)
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__Keio:14734 Length = 701 Score = 874 bits (2257), Expect = 0.0 Identities = 437/701 (62%), Positives = 540/701 (77%), Gaps = 19/701 (2%) Query: 8 KHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMKLDP 67 K++ W +L ++GAF L +AL RGE I+ALWIVVASV +YL+AYR+Y LYIA+ V+ +DP Sbjct: 6 KYLVWTVLSVMGAFALGYIALNRGEQINALWIVVASVCIYLIAYRFYGLYIAKNVLAVDP 65 Query: 68 TRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVV 127 TR TPAV +NDGL+YVPT++ VLFGHHFAAIAGAGPLVGPVLAAQMGYLPG +WLLAGVV Sbjct: 66 TRMTPAVRHNDGLDYVPTDKKVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMIWLLAGVV 125 Query: 128 LAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIVVKA 187 LAGAVQDFMVLF+S+RR+G SLGE++KEEMGP G IAL CF+IM+IILAVLA+IVVKA Sbjct: 126 LAGAVQDFMVLFVSTRRDGRSLGELVKEEMGPTAGVIALVACFMIMVIILAVLAMIVVKA 185 Query: 188 LAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHDPYW 247 L SPWG +TV T+P+ALFMGIY+R++RPGR+GEVSVIG+V L+ +I GG +A P W Sbjct: 186 LTHSPWGTYTVAFTIPLALFMGIYLRYLRPGRIGEVSVIGLVFLIFAIISGGWVAESPTW 245 Query: 248 GPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLNPEL 307 P F +T+ L+GY FV+A+LPVWL+LAPRDYL+TFLKIG IVGLA+GI+++ P L Sbjct: 246 APYFDFTGVQLTWMLVGYGFVAAVLPVWLLLAPRDYLSTFLKIGTIVGLAVGILIMRPTL 305 Query: 308 KMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARFIGY 367 MPA+T+++DGTGP+W G LFPFLFITIACGAVSGFHALISSGTTPK+LANE A FIGY Sbjct: 306 TMPALTKFVDGTGPVWTGNLFPFLFITIACGAVSGFHALISSGTTPKMLANEGQACFIGY 365 Query: 368 GAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQLKDV 427 G MLMESFVAIMALV+A II+PG+YFAMN+P A L AP A DV Sbjct: 366 GGMLMESFVAIMALVSACIIDPGVYFAMNSPMAVL--------------AP---AGTADV 408 Query: 428 TAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL-PMADM 486 A AA VSSWGF I+P+ + Q A ++GE S+++RAGGAPTLAVG+A++ H L M D+ Sbjct: 409 VASAAQVVSSWGFSITPDTLNQIASEVGEQSIISRAGGAPTLAVGMAYILHGALGGMMDV 468 Query: 487 GFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGL 546 FWYHF ILFEALFILTA+DAGTR+ RFMLQDLLG P LK+TDSL A ++ TA CV Sbjct: 469 AFWYHFAILFEALFILTAVDAGTRAARFMLQDLLGVVSPGLKRTDSLPANLLATALCVLA 528 Query: 547 WGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVPAVW 606 WGY L+QGVVDPLGG+ +LWPLFGI+NQMLA +AL+L VVL KMKR +Y WV +VP W Sbjct: 529 WGYFLHQGVVDPLGGINTLWPLFGIANQMLAGMALMLCAVVLFKMKRQRYAWVALVPTAW 588 Query: 607 LLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLTAQQIANMNHIVVNNYTNAG 666 LLICT A K FS + ++ GF +A++++ I +G + + + +V NN +AG Sbjct: 589 LLICTLTAGWQKAFSPDAKV-GFLAIANKFQAMIDSGNIPSQYTESQLAQLVFNNRLDAG 647 Query: 667 LSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707 L+I F++VV + + KT LA K T KETPY P+PE Sbjct: 648 LTIFFMVVVVVLALFSIKTALAALKDPKPTAKETPYEPMPE 688 Lambda K H 0.327 0.142 0.440 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: 1469 Number of extensions: 64 Number of successful extensions: 4 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: 716 Length of database: 701 Length adjustment: 39 Effective length of query: 677 Effective length of database: 662 Effective search space: 448174 Effective search space used: 448174 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 (21.7 bits) S2: 55 (25.8 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