Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate PfGW456L13_2351 Permeases of the major facilitator superfamily
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2351 Length = 436 Score = 249 bits (637), Expect = 1e-70 Identities = 161/435 (37%), Positives = 241/435 (55%), Gaps = 42/435 (9%) Query: 3 QTSSPPTPKGIWKVIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLGT 61 Q SS P + A+ GT+IEWYDFYI+ A A + F+ + + +A GT Sbjct: 4 QASSQPR-----RAAAAAFIGTMIEWYDFYIYATAAALVFGALFFPSDDKLFSTMAAFGT 58 Query: 62 FAVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILI 121 FAVGF RP G IVFG IGD +GRK + +IT+ +MG T IGLLPT +GA A ++LI Sbjct: 59 FAVGFFARPLGGIVFGHIGDRIGRKKSLIITLLMMGVVTVCIGLLPTYAQIGAAAPVLLI 118 Query: 122 TMRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLIS-LGVILITRISL 180 +RI+QG+A+GG++GGA EHAP+G+R F+ S+ Q + GL++S L +TR L Sbjct: 119 LLRIVQGIAVGGEWGGAVLMAGEHAPKGRRNFFASFAQLGSPAGLILSLLAFSAVTR--L 176 Query: 181 GEADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYN 240 E D WGWRLPF+AS LL+++ L IR + ESP F L + SKN KE Sbjct: 177 PEEDLMSWGWRLPFLASSLLLLVGLAIRLGVNESPEF--LASRELASKNKRKEQAPVMEV 234 Query: 241 LR--W--VLIALFGATMGQGVVWYTGQFYALFYLQKIF--NTPLIDSNLIVGAALLLSMP 294 LR W +L+ + T+G V++T F + Q++ + +++ +V P Sbjct: 235 LRTAWRPLLLCIGANTLGIAGVYFTNTFMIAYTTQQLELPRSLILECLFVVAIIQFCIQP 294 Query: 295 FFVFFGSLSDRIGRKKVMLSGMLLAVLTYYPIYGLM-AAFAPTDPGQHFLFAYIGYNPVI 353 + ++++IG + + LLA+ + YP++ L+ +A AP +I Sbjct: 295 LAAW---VAEKIGATRFLCLVSLLAMASPYPMFVLVSSAQAPL---------------II 336 Query: 354 LGLLVFIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILIN 413 LG + + V+ + Y IA ++ +F T++RYT++SL Y I V GGL P+IG +L Sbjct: 337 LG--IALAVVCMASFYAVIAGYVSGMFETRVRYTAISLAYQICGAVAGGLTPLIGTLL-- 392 Query: 414 ATGNDFAGLWWPMAI 428 + F G WWPMA+ Sbjct: 393 --AHRFVGQWWPMAV 405 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: 609 Number of extensions: 38 Number of successful extensions: 8 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: 436 Length adjustment: 33 Effective length of query: 435 Effective length of database: 403 Effective search space: 175305 Effective search space used: 175305 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