Align Uncharacterized protein (characterized, see rationale)
to candidate Dsui_3482 Dsui_3482 Na+/H+ dicarboxylate symporter
Query= uniprot:A0A0C4Y5S4 (436 letters) >FitnessBrowser__PS:Dsui_3482 Length = 437 Score = 532 bits (1371), Expect = e-156 Identities = 269/415 (64%), Positives = 337/415 (81%), Gaps = 1/415 (0%) Query: 1 MKLNRLPTLIFIAMLLGVLAGTAAHHYAPDPAAAKSIADHLSILTDVFLRMIKMIIGPLV 60 MK+N+L T I +AML GV G A + APD A+AK IA + SILTD+FLR+IKMII PL+ Sbjct: 1 MKMNKLTTWIVLAMLAGVGVGYACNTMAPDAASAKEIAGYFSILTDIFLRLIKMIIAPLI 60 Query: 61 FATLVSGIASMGDGKAVGRIGMKAMAWFIAASITSLLLGLLMANLLRPGDGMNLALPAAD 120 FATLV+G+A+MGD KAVGR+G +A+ WFI AS SL +GLL AN+L+PG +++ LP + Sbjct: 61 FATLVAGLANMGDAKAVGRVGGRALGWFICASFCSLFIGLLFANVLQPGHALSVPLPESA 120 Query: 121 AASNLKTGALNLREFIAHMFPKSFVEAMATNEILQIVVFSLFFGFALGTLKDGIGKPVLA 180 A NLKT ALNL++FI H+FPKS +EAMA NE+LQI+VF++FFG ALG L + + ++ Sbjct: 121 AGLNLKTSALNLKDFITHVFPKSIMEAMAGNEVLQILVFAVFFGLALGHLHNQAARSLVN 180 Query: 181 GIEGLSHVMLKITNYVMAFAPVGVFGAVAAVITAEGLGVLVVYAKLLGAVYLSLALLWVA 240 ++ + HVMLK+T+YVM FAP GVFGAVA IT GLG+L+V+ K + + Y++LA LW Sbjct: 181 TMDEVVHVMLKVTDYVMRFAPFGVFGAVAGAITTNGLGMLLVFGKFMLSFYVALAALWAL 240 Query: 241 LIAGGYFFLGRDVFRLLKMVRAPLMIGFATASSESAYPKVIEQLGRFGVKERITGFVLPL 300 LI G+ LG+DVFRL+K+VR PL++GF+TASSES YPK++EQL +FG+K R+TGFVLPL Sbjct: 241 LILAGFIVLGKDVFRLIKLVRGPLLVGFSTASSESVYPKLMEQLEKFGIKTRVTGFVLPL 300 Query: 301 GYSFNLDGSIMYTSFAALFVAQVYGIHLSLSQQVTMLLVLLVTSKGIAGVPRASLVVVAA 360 GYSFNLDGS+MYT+F ALF+AQ Y I +SL+ Q+TMLLVL+V+SKGIAGVPRASLVVVAA Sbjct: 301 GYSFNLDGSMMYTTFLALFIAQAYDIPMSLTAQITMLLVLMVSSKGIAGVPRASLVVVAA 360 Query: 361 VLPMFGLPEAGILLVLGIDHVLDMGRTVTNVLGNAIATTVVAKSEGAIGAPVPEE 415 VLPMF LPEAG+LLVLGIDH LDMGRTVTNVLGN+IAT VVAK EGAI PV EE Sbjct: 361 VLPMFNLPEAGLLLVLGIDHFLDMGRTVTNVLGNSIATAVVAKWEGAID-PVSEE 414 Lambda K H 0.325 0.141 0.401 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: 552 Number of extensions: 18 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: 436 Length of database: 437 Length adjustment: 32 Effective length of query: 404 Effective length of database: 405 Effective search space: 163620 Effective search space used: 163620 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 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