Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate 17584 b3523 predicted transporter (NCBI)
Query= TCDB::Q7X4L6 (552 letters) >FitnessBrowser__Keio:17584 Length = 440 Score = 206 bits (524), Expect = 1e-57 Identities = 131/372 (35%), Positives = 200/372 (53%), Gaps = 17/372 (4%) Query: 3 TIEGRAAPAPITSEERRVIFASSLGTVFEWYDFYLAGSLAIYI-SRTFFSGVNPAAGFVF 61 T++ PI S + V+ AS +GT E++DFY+ + A+ + FF +P A + Sbjct: 7 TLDHEQEYTPINSRNK-VLVASLIGTAIEFFDFYIYATAAVIVFPHIFFPQGDPTAATLQ 65 Query: 62 TLLGFAAGFAVRPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAP 121 +L FA F RP G+ VFG GD +GRK T +A++L MG+ST V+GLLPGY TIG+ AP Sbjct: 66 SLATFAIAFVARPIGSAVFGHFGDRVGRKATLVASLLTMGISTVVIGLLPGYATIGIFAP 125 Query: 122 VVFIAMRMLQGLALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVR 181 ++ R QGL LGGE+GGAA E+AP KR + ++ Q A +G F + L + Sbjct: 126 LLLALARFGQGLGLGGEWGGAALLATENAPPRKRALYGSFPQLGAPIGFFFANGTFLLLS 185 Query: 182 SLLNEDTFAAWGWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQ 241 LL ++ F +WGWRVPF+ S VL+ + +++R+ LHESPVFE++ K K PL Sbjct: 186 WLLTDEQFMSWGWRVPFIFSAVLVIIGLYVRVSLHESPVFEKVAKAKKQVKIPLGTLL-- 243 Query: 242 WKNLKIVLLALFGLTAGQAVVWYTGQFYTLFFLTQTLKVD-GTSANMLVAVALLIGTPFF 300 K++++ +L F + A ++Y Y++ F T V G N ++ + ++ F Sbjct: 244 TKHVRVTVLGTFIMLA-TYTLFYIMTVYSMTFSTAAAPVGLGLPRNEVLWMLMMAVIGFG 302 Query: 301 LFF---GSLSDKIG-RKPIIMAGCLIAALTYFPLFKALAHYTNPKLEAATLQAPITMIAD 356 + G L+D G RK +++ LI F F L NP L A L ++++ Sbjct: 303 VMVPVAGLLADAFGRRKSMVIITTLIILFALF-AFNPLLGSGNPILVFAFLLLGLSLM-- 359 Query: 357 PSECSFQFNPVG 368 F P+G Sbjct: 360 ----GLTFGPMG 367 Score = 38.5 bits (88), Expect = 5e-07 Identities = 16/46 (34%), Positives = 30/46 (65%), Gaps = 3/46 (6%) Query: 455 ILILTILVLYVTMV---YGPLAAMLVEMFPARIRYTSMSLPYHIGN 497 IL+ L+L ++++ +GP+ A+L E+FP +RYT S Y++ + Sbjct: 346 ILVFAFLLLGLSLMGLTFGPMGALLPELFPTEVRYTGASFSYNVAS 391 Lambda K H 0.325 0.139 0.420 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: 666 Number of extensions: 53 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 552 Length of database: 440 Length adjustment: 34 Effective length of query: 518 Effective length of database: 406 Effective search space: 210308 Effective search space used: 210308 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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