Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate GFF1418 PS417_07205 LysR family transcriptional regulator
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__WCS417:GFF1418 Length = 439 Score = 243 bits (621), Expect = 7e-69 Identities = 153/444 (34%), Positives = 246/444 (55%), Gaps = 54/444 (12%) Query: 2 MQTSSPPTPKGIWKVIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLG 60 M+ S+ P P+ + A+ GT+IEWYDFYI+ A A F+ + + +A G Sbjct: 1 MKPSASPQPR---RAAAAAFIGTMIEWYDFYIYATAAALVFGQLFFPSDDKLFSTMAAFG 57 Query: 61 TFAVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIIL 120 TFAVGF RP G IVFG IGD +GRK + +IT+ +MG T IGLLPT +GA A ++L Sbjct: 58 TFAVGFFARPLGGIVFGHIGDRIGRKKSLVITLVMMGVVTVCIGLLPTYAQIGAAAPVLL 117 Query: 121 ITMRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLIS-LGVILITRIS 179 + +R++QG+A+GG++GGA EHAP+G+R F+ S+ Q + GL++S L +TR Sbjct: 118 VLLRVVQGIAVGGEWGGAVLMAGEHAPKGRRNFFASFAQLGSPAGLILSLLAFSAVTR-- 175 Query: 180 LGEADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLK----DTKAVSKN--PLKE 233 L E + WGWR+PF+AS LL+++ L IR + ESP F + K +A+ K+ P+ E Sbjct: 176 LPEDELLSWGWRVPFLASALLLVVGLAIRLGVNESPEFLEDKALAEKARAIKKDQAPVIE 235 Query: 234 SFANPYNLRWVLIALFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSM 293 + R +L+ + T+G V++T F + Q+ L + +L+L Sbjct: 236 VLRTAW--RPLLLCIGANTLGIAGVYFTNTFMIAYSTQQ----------LGLPRSLILEC 283 Query: 294 PFFV---------FFGSLSDRIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLF 344 FFV +++++G + + + +LA+ + YP++ L+++ Sbjct: 284 LFFVAIIQFCVQPLAAWVAEKVGATRFLCAMTVLAMASPYPMFVLVSS------------ 331 Query: 345 AYIGYNPVILGLLVFIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLV 404 G P+I+ L + + V+ + Y IA F+ LF T++RYT++SL Y + + GGL Sbjct: 332 ---GQAPLII-LGIALAVVCMASFYAVIAGFVSGLFETRVRYTAISLAYQVCGALAGGLT 387 Query: 405 PMIGLILINATGNDFAGLWWPMAI 428 P+IG L +++ G WWPMA+ Sbjct: 388 PLIGTWL----AHEYQGQWWPMAV 407 Lambda K H 0.328 0.144 0.450 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: 614 Number of extensions: 40 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: 468 Length of database: 439 Length adjustment: 33 Effective length of query: 435 Effective length of database: 406 Effective search space: 176610 Effective search space used: 176610 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: 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