Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate AO353_25255 AO353_25255 carbon starvation protein A
Query= SwissProt::P39396 (716 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25255 Length = 685 Score = 979 bits (2531), Expect = 0.0 Identities = 483/705 (68%), Positives = 582/705 (82%), Gaps = 25/705 (3%) Query: 5 KIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMK 64 ++ KH+ W + ++GAF L+VVALRRGE I+ALWIVVA+V++YLVAYRYYSL+IA KVM+ Sbjct: 3 RLAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQ 62 Query: 65 LDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLA 124 LDP RATPAV+NNDGL+YVPTN+++LFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWL+A Sbjct: 63 LDPGRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIA 122 Query: 125 GVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIV 184 GVVLAGAVQDFMVLF+S+RRNG SLG+M++EEMG VPGTIALFGCFLIMIIILAVLALIV Sbjct: 123 GVVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIV 182 Query: 185 VKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHD 244 VKALA+SPWG+FTV +T+PIA+FMG+YMR+IRPGR+GE+SV+G++LL+ SI+ GG IA D Sbjct: 183 VKALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAAD 242 Query: 245 PYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLN 304 P W A +F IT+ LIGY FV+A++PVWLILAPRDYL+TFLKIG I+ LA+GI++ Sbjct: 243 PVWAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITM 302 Query: 305 PELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARF 364 PELKMPA+TQ+IDGTGP+WKG LFPFLFITIACGAVSGFHALI+SGTTPKLLA+E AR+ Sbjct: 303 PELKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARY 362 Query: 365 IGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQL 424 IGYG MLMESFVAIMA+VAAS+IEPG+YFAMN+P A +GG+ Sbjct: 363 IGYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAA----------IVGGD--------- 403 Query: 425 KDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVLPMA 484 A TVSSWGF+I+PE + AKDIGE +VL RAGGAPTLAVGIA + H VLP Sbjct: 404 ---VVQVAQTVSSWGFMITPEALQAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGE 460 Query: 485 D-MGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGC 543 + M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P LK+T+S A +I TAGC Sbjct: 461 NTMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGC 520 Query: 544 VGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVP 603 V +WGYLLYQGV+DPLGG+ +LWPLFGISNQMLA +AL+L TVVLIKMKR +YIWVT++P Sbjct: 521 VAMWGYLLYQGVIDPLGGINTLWPLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLP 580 Query: 604 AVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNY 662 A WLLICTT A +KLF NP + GF +A +Y + +ANG L A+ I M H++ N Y Sbjct: 581 AAWLLICTTTAGFIKLFDANPAI-GFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAY 639 Query: 663 TNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIPE 707 TNA L+ LFL VV+SI+FY K ++ S +RTDKE+P+ IPE Sbjct: 640 TNATLTALFLFVVFSILFYAIKVGISAWGSKERTDKESPFQAIPE 684 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: 1517 Number of extensions: 69 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: 685 Length adjustment: 39 Effective length of query: 677 Effective length of database: 646 Effective search space: 437342 Effective search space used: 437342 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