Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate BWI76_RS03450 BWI76_RS03450 MFS transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Koxy:BWI76_RS03450 Length = 454 Score = 238 bits (606), Expect = 4e-67 Identities = 145/428 (33%), Positives = 247/428 (57%), Gaps = 33/428 (7%) Query: 16 VIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74 V+ + +GT IE+YDF+I+G A A S F+ +P+ ++ T ++ F+ RP GAI Sbjct: 30 VLGSGLSGTTIEFYDFFIYGTAAALVFPSLFFPNLSPLMALLVSFLTLSITFVSRPIGAI 89 Query: 75 VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134 VFG GD +GRK + ++++ IMG TF IGL+P+ + +G A +ILI +R+ QG A+GG+ Sbjct: 90 VFGHYGDKIGRKKSLVLSLMIMGISTFFIGLIPSYNTIGNAAPLILIFLRLCQGFAIGGE 149 Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPF 194 +GGA T + E+AP+ +RGF+ +++Q GL I+ GV + + L E D WGWR+PF Sbjct: 150 WGGATTLITEYAPRHRRGFFGTFVQLGNVLGLFIATGVFALV-VMLPEEDLMSWGWRVPF 208 Query: 195 MASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESF----ANPYNLRWVLIALFG 250 + SI L+ + ++IR ++E+P+FQ+ + + + ++ F ++ + V +A+ G Sbjct: 209 LLSIALLFVGMFIRSRIEETPVFQENQKQQQNAPKAAEQKFPILTVLKHHRKAVFLAM-G 267 Query: 251 ATMGQGVV-WYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRK 309 MG+ V+ W T F+ + +++ T N ++ A + + F FFG LSD+IGR+ Sbjct: 268 MRMGEIVLGWLTVAFFMSYVTRELNFTRETALNGLL-LASFVGIFTFPFFGWLSDKIGRR 326 Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPG--QHFLFAYIGYNPVILGLLVFIQVIYVTM 367 V L+G + ++ +P++ ++ D G + F+FA V LG++ +Q Sbjct: 327 PVYLAGAAITLIFAFPLFWMI------DSGSVKMFMFATTFCYSVGLGMMFSVQ------ 374 Query: 368 VYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMA 427 AF ELF T +RYT +SL + + N + GGL PMIG +L+ +G G WP++ Sbjct: 375 -----PAFFSELFDTSVRYTGVSLGFQLAN-IVGGLTPMIGTLLLVWSG----GASWPIS 424 Query: 428 IAGICLVV 435 + C+ + Sbjct: 425 LFLACMAL 432 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: 644 Number of extensions: 45 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: 454 Length adjustment: 33 Effective length of query: 435 Effective length of database: 421 Effective search space: 183135 Effective search space used: 183135 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