Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate PfGW456L13_1444 Carbon starvation protein A
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1444 Length = 688 Score = 980 bits (2533), Expect = 0.0 Identities = 485/702 (69%), Positives = 580/702 (82%), Gaps = 25/702 (3%) Query: 8 KHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMKLDP 67 +H+PW++L I+GA L VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA VM+LD Sbjct: 9 RHLPWLVLAIVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANNVMQLDA 68 Query: 68 TRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLAGVV 127 RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL+AGVV Sbjct: 69 RRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV 128 Query: 128 LAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIVVKA 187 LAGAVQDFMVLF+S+RRNG SLG+M++EEMG +PGTIALFGCFLIMIIILAVLALIVVKA Sbjct: 129 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVVKA 188 Query: 188 LAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHDPYW 247 LAESPWG+FTV +T+PIA+FMGIYMR+IRPGR+GE+SVIG++LL+ SI+ GG IA DP W Sbjct: 189 LAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVLLLLGSIWLGGQIAADPVW 248 Query: 248 GPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLNPEL 307 A +F IT+ LIGY FV+A+LPVWLILAPRDYL+TFLKIG IV LA+GI+V PEL Sbjct: 249 AKAFSFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILVTMPEL 308 Query: 308 KMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARFIGY 367 KMPA+TQ++DGTGP+WKG LFPFLFITIACGAVSGFHALISSGTTPKLL NET+AR+IGY Sbjct: 309 KMPALTQFVDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYIGY 368 Query: 368 GAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQLKDV 427 G MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +G DV Sbjct: 369 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVG---------------------GDV 407 Query: 428 TAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLPMAD-M 486 A A A VS+WGF I+PE + A DIGE ++L RAGGAPTLAVGIA + H VLP + M Sbjct: 408 VAVATA-VSNWGFAITPEALQAVAHDIGETTILARAGGAPTLAVGIAQILHSVLPGENTM 466 Query: 487 GFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGCVGL 546 FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S A +I TAGCV + Sbjct: 467 AFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAM 526 Query: 547 WGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVPAVW 606 WG+LLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+LGTVVLIKMKR +Y+WVT++PAVW Sbjct: 527 WGWLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLGTVVLIKMKRQRYVWVTMLPAVW 586 Query: 607 LLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNYTNA 665 LLICTT A +KLF NP + GF +A +Y + +ANG L A+ I M H++ N YTNA Sbjct: 587 LLICTTTAGFIKLFDANPAI-GFLSLAKKYSDALANGQILAPAKDITQMQHVIFNAYTNA 645 Query: 666 GLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707 L+ LFL VV+SI+FY K +A +RTDKE+P+ +P+ Sbjct: 646 TLTALFLFVVFSILFYALKVGIAAWGKKERTDKESPFQALPD 687 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: 1549 Number of extensions: 73 Number of successful extensions: 7 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: 688 Length adjustment: 39 Effective length of query: 677 Effective length of database: 649 Effective search space: 439373 Effective search space used: 439373 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: 54 (25.4 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