Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate WP_057507757.1 ABB28_RS05925 MFS transporter
Query= TCDB::M1Q159 (468 letters) >NCBI__GCF_001431535.1:WP_057507757.1 Length = 430 Score = 215 bits (547), Expect = 3e-60 Identities = 148/452 (32%), Positives = 220/452 (48%), Gaps = 49/452 (10%) Query: 5 SSPPTPKGI-WKVIFASSAGTVIEWYDFYIFGALATTLASK-FYNTGTPIGDIIAWLGTF 62 S PPTP +V+ AS GT IE++DFYI+ A + F+ + ++ L TF Sbjct: 9 SIPPTPANSPQRVLLASLIGTTIEFFDFYIYATAAVLVFPHLFFPESSDKAAMLQSLATF 68 Query: 63 AVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILIT 122 AV F+ RP G+ VFG GD +GRK T + + MG T LIGLLPT +G WA +L Sbjct: 69 AVAFIARPVGSAVFGHFGDRIGRKATLVAALLTMGLSTVLIGLLPTHAQIGLWAPALLAL 128 Query: 123 MRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGE 182 R QGL LGG++GGA E+AP GKR +Y + Q A G L+S G+ LI L Sbjct: 129 CRFGQGLGLGGEWGGAVLLATENAPPGKRAWYGMFPQLGAPLGFLLSAGIFLILGRLLSA 188 Query: 183 ADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLR 242 DF +WGWR+PF+AS LLV L LW+R + E+P FQ+ D A K P+ LR Sbjct: 189 DDFLQWGWRIPFVASALLVGLGLWVRLNIHETPAFQKALDAHARVKLPMLTV------LR 242 Query: 243 WVLIALFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAA----LLLSMPFFVF 298 + + T+G + LFYL +F L ++G + LLL M +F Sbjct: 243 DHAMPMLLGTLGAFAT------FVLFYLMTVF--ALGHGTAVLGYSREQFLLLQMVGILF 294 Query: 299 FGS-------LSDRIGRKKVML--SGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGY 349 F + DR G ++ M+ SG+++ ++G++ A + A++ Sbjct: 295 FAAGIPISARYGDRWGTRRTMIIASGLIV-------VFGVLLAPMFQAGSPWMVLAFLSL 347 Query: 350 NPVILGLLVFIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGL 409 ++GL YGP FL E++P ++RYT SL +++ + P + Sbjct: 348 GLFLMGL-----------TYGPCGTFLAEIYPVEVRYTGASLSFNLAGILGAAPAPYLAT 396 Query: 410 ILINATGNDFAGLWWPMAIAGICLVVGFLLIK 441 L G G + + IA + + L ++ Sbjct: 397 WLAERFGLVAVGYY--LCIAALVTICALLALQ 426 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: 686 Number of extensions: 50 Number of successful extensions: 5 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: 430 Length adjustment: 33 Effective length of query: 435 Effective length of database: 397 Effective search space: 172695 Effective search space used: 172695 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 24 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