Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate Ga0059261_3322 Ga0059261_3322 Arabinose efflux permease
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Korea:Ga0059261_3322 Length = 445 Score = 196 bits (497), Expect = 2e-54 Identities = 137/424 (32%), Positives = 202/424 (47%), Gaps = 34/424 (8%) Query: 19 ASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAIVFGR 78 A S G +IEWYDFY + A AS F+ G ++ +A GFL+RP G FGR Sbjct: 39 AGSVGNLIEWYDFYAYAYTALYFASAFFPAGDRTAQLLNVAAIYAAGFLIRPLGGWFFGR 98 Query: 79 IGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYGGA 138 D GR+ + ++ +MG+ + L+G+LPT +GA A +L+ R++QG + GGQYG A Sbjct: 99 YADRHGRRAAMIASVVLMGAGSLLVGVLPTYATIGAAAPALLLVARLMQGFSTGGQYGAA 158 Query: 139 ATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPFMASI 198 AT+++E A GKRGFY S+ T G L +L V+ + ++ E EWGWRLPF+ Sbjct: 159 ATYLSEIAEPGKRGFYASFQFVTLIGGQLFALLVVFALQSTMSETAIREWGWRLPFLLGA 218 Query: 199 LLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQGVV 258 +L + + R + E+ +K LK F +P +V++AL A V Sbjct: 219 VLAGVFILFRDVMHET----AEPASKGEDAGSLKALFQHP-RAMFVVMALSAA---GAVT 270 Query: 259 WYTGQFYALFYLQKIFNTPLIDSN---LIVGAALLLSMPFFVFFGSLSDRIGRKKVMLSG 315 YT Y YL + ++ LIV A LL P G+LSDRIGR+ +L Sbjct: 271 LYTFTTYMQKYLVNTAGMDVASASRTMLIVTFAFLLLQP---VLGTLSDRIGRRTNLLI- 326 Query: 316 MLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVI--LGLLVFIQVIYVTMVYGPIA 373 G M FA L IG + GLLVF + ++ Sbjct: 327 ----------FSGGMTLFAVP------LLGAIGQAQTMWSAGLLVFAALAIMSFYTSVSG 370 Query: 374 AFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAGICL 433 F ELFP ++R + L + I + +FGG L+L G++ W+ A+ + Sbjct: 371 LFKAELFPARVRALGVGLGHAIASAIFGGTAEWAALML-KQMGHEGLFAWYVSAVCAVAF 429 Query: 434 VVGF 437 VV + Sbjct: 430 VVAW 433 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: 599 Number of extensions: 37 Number of successful extensions: 4 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: 445 Length adjustment: 33 Effective length of query: 435 Effective length of database: 412 Effective search space: 179220 Effective search space used: 179220 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