Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate WP_011652458.1 RL_RS15195 MFS transporter
Query= TCDB::Q7X4L6 (552 letters) >NCBI__GCF_000009265.1:WP_011652458.1 Length = 416 Score = 117 bits (292), Expect = 1e-30 Identities = 95/335 (28%), Positives = 152/335 (45%), Gaps = 38/335 (11%) Query: 13 ITSEERRVIFASSLGTVFEWYDFYLAGSLAIYISRTFFSGVNPAAGFVFTLLGFAAGFAV 72 +T ++R + AS LG + +DF++ + YI+ F + V + +F L A+ Sbjct: 10 LTPQQRNTVIASYLGWTLDAFDFFILVFVLKYIAEEFHTDVPAVSVAIFLTL------AM 63 Query: 73 RPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQG 132 R GA+VFG D GR+ T +A +LL + F+ G G +F+ R L G Sbjct: 64 RALGALVFGLAADRYGRRITLMADVLLYSIFEFLTGFSTGL--------TMFLVFRALYG 115 Query: 133 LALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNEDTFAAW 192 +A+GGE+G A+ V E P RG + +Q G I+ +V + F Sbjct: 116 IAMGGEWGVGASLVMETVPEESRGIVSGILQAGYPSGYLIASIVFFLL--------FPVI 167 Query: 193 GWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNLKIVLLAL 252 GWR F V + + ++IR + ESP F + +A G+ + +N+ + + A+ Sbjct: 168 GWRGMFFVGALPALLVLYIRRNVEESPAFLKRQATGRRPFLTVLR-----ENIPLFIWAV 222 Query: 253 FGLTAGQAVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALLIGTPFF---LFFGSLSDK 309 +TA T Y F TQ S+ + A+A++ LFFG+LS + Sbjct: 223 LLMTAFNFFSHGTQDIYPTFLETQR----NYSSYTVGAIAIVYNIGAICGGLFFGALSQR 278 Query: 310 IGRKPIIMAGCLIAALTYFPLFKALAHYTNPKLEA 344 IGR+ I +IAAL P+ A+ P L A Sbjct: 279 IGRRRAI----VIAALIAVPVAPLWAYAPGPVLLA 309 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: 549 Number of extensions: 31 Number of successful extensions: 6 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: 552 Length of database: 416 Length adjustment: 34 Effective length of query: 518 Effective length of database: 382 Effective search space: 197876 Effective search space used: 197876 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: 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