Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 18105 b4077 glutamate/aspartate:proton symporter (NCBI)
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Keio:18105 Length = 437 Score = 364 bits (935), Expect = e-105 Identities = 179/419 (42%), Positives = 285/419 (68%), Gaps = 20/419 (4%) Query: 6 NLTVQVITAVIIGVIVGLV---------WPDVGKEMKPLGDTFINAVKMVIAPIIFFTIV 56 +L Q++ A+++G+++G W V + P GD FI+ +KM++ PI+ T+V Sbjct: 7 SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNL-LSPAGDIFIHLIKMIVVPIVISTLV 65 Query: 57 LGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQY 116 +GIA +GD K++G++G K IYFEV+TT+A+I+G+ + N+ +PGAG+D S+L D+S+Y Sbjct: 66 VGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKY 125 Query: 117 ------TQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKS 170 Q+ GI + I +VP+N+V + AKG++L ++FFS+LFG+GL++L + Sbjct: 126 QSTTEAVQSSSHGI--MGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHRE 183 Query: 171 -VIDFFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFL 229 ++ F +S FK+ +MR AP+G F +A T+ +FG S+ PLA L++ V+ + Sbjct: 184 PLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILF 243 Query: 230 FVFVALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGL 289 F V L I+ +L G S+W +R +KDEL++ T+SSESVLPR+++KME YG S+ Sbjct: 244 FALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSF 303 Query: 290 VIPTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFI 349 V+PTGYSFNLDG+++Y S+A +F+AQ++G+DLSI Q+I ++L LM+TSKG AGV G F+ Sbjct: 304 VVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFV 363 Query: 350 VLASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAKSI 408 VL +TL ++ IPLEGLA + GVDR + R +N++GN +A +++AK E++FD K++ Sbjct: 364 VLLATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKAL 421 Lambda K H 0.326 0.143 0.408 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: 509 Number of extensions: 17 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: 421 Length of database: 437 Length adjustment: 32 Effective length of query: 389 Effective length of database: 405 Effective search space: 157545 Effective search space used: 157545 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 (21.6 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