Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate SMc01869 SMc01869 transport transmembrane protein
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Smeli:SMc01869 Length = 436 Score = 219 bits (557), Expect = 2e-61 Identities = 150/432 (34%), Positives = 220/432 (50%), Gaps = 44/432 (10%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASK-FYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 +V+FAS GT IE++DFY++ A + F+ P ++ L TF++ F RP GA Sbjct: 25 RVLFASLVGTTIEFFDFYVYATAAVIIFPHLFFPAADPTSAMLQSLATFSIAFFARPLGA 84 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 ++FG GD +GRK T + + MG T +IGLLPT +G A ++L R QGL LGG Sbjct: 85 VIFGHFGDRIGRKATLVAALMTMGISTVVIGLLPTYSTIGVVAPLLLALCRFGQGLGLGG 144 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGA E+AP+GKR +Y + Q A G ++S G LI + E F WGWR+P Sbjct: 145 EWGGAVLLATENAPEGKRSWYAMFPQLGAPIGFILSAGTFLILGEVMSEEAFLAWGWRVP 204 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATM 253 F+AS+LLVI+ L++R + E+P FQ+ D + P+ F + + R +++ F A Sbjct: 205 FIASVLLVIVGLYVRLKITETPEFQKAIDKHERVEVPVAAIFRS--HKRSLVLGTFVAL- 261 Query: 254 GQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAA--LLLSMPFFVFF-------GSLSD 304 + LFYL +F+ + L LL+ M VFF G LSD Sbjct: 262 ---------ATFVLFYLMTVFSLSWGTTKLGYSREQFLLVQMTGVVFFGLMIPVSGILSD 312 Query: 305 RIGRKKVMLSGMLLAVLTYYPIYGL-MAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVI 363 R GR+ V L+ ++GL MA + G F+F+ +G LGL+ Sbjct: 313 RFGRRLV-----LVLTTIGIGVFGLFMAPLLSSGLGGAFVFSIVG-----LGLM------ 356 Query: 364 YVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFG-GLVPMIGLILINATGNDFAGL 422 + YGPI A L FPT +RYT S+ +++ G+FG L P I L G Sbjct: 357 --GLTYGPIGAALAAPFPTAVRYTGASMTFNLA-GIFGASLAPYIATWLATNYSLGHVG- 412 Query: 423 WWPMAIAGICLV 434 ++ +A A I LV Sbjct: 413 YYLLAAASITLV 424 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: 659 Number of extensions: 42 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: 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