Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate CCNA_01852 CCNA_01852 major facilitator superfamily transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Caulo:CCNA_01852 Length = 446 Score = 126 bits (317), Expect = 1e-33 Identities = 118/420 (28%), Positives = 187/420 (44%), Gaps = 56/420 (13%) Query: 23 GTVIEWYDFYIFGALATTLASKFYNTGTPIGD----IIAWLGTFAVGFLVRPFGAIVFGR 78 G E++DF+++ A+A+ L F P D ++ G FA+ F+ RPFG+++FG Sbjct: 39 GRTSEFFDFFVY-AIASVLV--FPQLVFPFVDRLTGVMLAFGLFALAFIARPFGSVIFGA 95 Query: 79 IGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYGGA 138 I GR I + ++G T +I +LP+ +G A L RI QGLAL G + G Sbjct: 96 IDQRYGRGVKLTIALFLLGGSTAVISMLPSFAAVGPIAIWALAACRIGQGLALAGAWDGM 155 Query: 139 ATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPFMASI 198 A+ +A +AP+ KRG+Y Q A FG +++ G+ +L ADF +WGWR PF A+ Sbjct: 156 ASLLALNAPENKRGWYAMIPQLGAPFGFMLASGLFAYFVATLAPADFLDWGWRYPFFAAF 215 Query: 199 LLVILSLWIRRALKESPLF------QQLKDTKAVSKNPLKESFANPYNLRWVLIALFGAT 252 + +++L+ R + + F ++L+ T+ S L+ N VLI F Sbjct: 216 AINVVALFARLRIVATEEFGALFEKRELRPTRVASL--LRAEGGN------VLIGAFAPL 267 Query: 253 MGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKKVM 312 +A+F+L +F PL L A L+ FG+L +G ++ Sbjct: 268 ----------ATFAMFHLVTVF--PLSWVVLHGDAQQALNFLRIELFGAL---VGVGGIL 312 Query: 313 LSGMLLAVLTYYP-------IYGLMAAFAP--TDPGQHFLFAYIGYNPVILGLLVFIQVI 363 SG + +T + G + AP D G AY+ ILGL Sbjct: 313 ASGWIADRITRQNQLALSALLIGAFSLLAPRLLDGGATGQTAYVVIGFAILGL------- 365 Query: 364 YVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLW 423 +G A + F + RYT +L + + G P+ L L + G GL+ Sbjct: 366 ----SFGQAAGAVSSGFSKRYRYTGAALTSDLSWLIGAGFAPLAALGLASLWGLPAIGLY 421 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: 607 Number of extensions: 37 Number of successful extensions: 2 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: 446 Length adjustment: 33 Effective length of query: 435 Effective length of database: 413 Effective search space: 179655 Effective search space used: 179655 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