Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate BWI76_RS02105 BWI76_RS02105 glutamate/aspartate:proton symporter GltP
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Koxy:BWI76_RS02105 Length = 437 Score = 364 bits (935), Expect = e-105 Identities = 175/415 (42%), Positives = 283/415 (68%), Gaps = 20/415 (4%) Query: 10 QVITAVIIGVIVGLV---------WPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIA 60 Q++ A+++G+++G W + + P GD FI+ +KM++ PI+ T+V+GIA Sbjct: 12 QILLALVLGILLGSYLHYHAESRDWL-ISNLLTPAGDIFIHLIKMIVVPIVISTLVVGIA 70 Query: 61 KMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQY---- 116 +GD K++G++G K IYFEV+TT+A+++G+ + N+ +PG+G+D S+L D+S+Y Sbjct: 71 GVGDAKQLGRIGAKTIIYFEVITTVAIVLGITLANVFQPGSGIDMSQLAAVDISKYQNTT 130 Query: 117 --TQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKS-VID 173 Q+ G+ + I +VP+N+V + AKGD+L ++FFS+LFG+GL++L + ++ Sbjct: 131 AEVQSHAHGL--MGTILSLVPTNIVASMAKGDMLPIIFFSVLFGLGLSSLPATHREPLVT 188 Query: 174 FFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFV 233 F +S FK+ +MR AP+G F ++ T+ FG S+ PLA L++ VY + F V Sbjct: 189 VFRSISETMFKVTHMVMRYAPVGVFALISVTVATFGFASLWPLAKLVILVYFAILFFALV 248 Query: 234 ALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPT 293 L I+ ++ G S+W +R +KDEL++ T+SSESVLPR+++KME YG S+ V+PT Sbjct: 249 VLGIVARVCGLSIWTLIRILKDELILAYSTASSESVLPRIIEKMEAYGAPASITSFVVPT 308 Query: 294 GYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLAS 353 GYSFNLDG+++Y S+A +F+AQ++G+DLSI Q+IT++L LM+TSKG AGV G F+VL + Sbjct: 309 GYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEITLVLTLMVTSKGIAGVPGVSFVVLLA 368 Query: 354 TLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAKSI 408 TL ++ IPLEGLA + GVDR + R +N++GN +A +++AK E++FD K++ Sbjct: 369 TLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKAL 422 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: 502 Number of extensions: 20 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