Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate PP_0137 PP_0137 glutamate/aspartate-proton DAACS transporter
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Putida:PP_0137 Length = 442 Score = 360 bits (925), Expect = e-104 Identities = 175/413 (42%), Positives = 276/413 (66%), Gaps = 13/413 (3%) Query: 6 NLTVQVITAVIIGVIVGLVWPDVGKE--------MKPLGDTFINAVKMVIAPIIFFTIVL 57 +L Q++ +++GV +G + E ++P GD FI +KM++ PI+ ++++ Sbjct: 7 SLAWQIVIGLVLGVAIGALLNHFSAEKAWWISNVLQPAGDIFIRLIKMIVVPIVISSLIV 66 Query: 58 GIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYT 117 GIA +GD KK+G +G K IYFEVVTT+A+++GL + N+ PGAG+D S L D+S+Y Sbjct: 67 GIAGVGDAKKLGSIGLKTIIYFEVVTTIAIVVGLVLANLFHPGAGIDMSTLGTVDISKYQ 126 Query: 118 QNGGQGID---WIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAAL-GEKGKSVID 173 + +IE + +++PSN+ A +G++L ++FFS++FG+GL++L E ++ Sbjct: 127 ATAAEVQHEHAFIETLLNLIPSNIFAALMRGEMLPIIFFSVMFGLGLSSLQAELRDPLVR 186 Query: 174 FFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFV 233 F VS FK+ IM APIG F +A T+ +FG S+ PLA L++ VY + F F+ Sbjct: 187 TFQAVSETMFKVTHMIMNYAPIGVFALIAVTVANFGFSSLLPLAKLVVLVYFAIAFFAFM 246 Query: 234 ALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPT 293 L ++ +L+GFS+ +R +KDEL++ TSSSE+VLPR+++KME+YG KS+ V+PT Sbjct: 247 VLGLVARLFGFSVIKIMRIMKDELILAYSTSSSETVLPRVIEKMEKYGAPKSICSFVVPT 306 Query: 294 GYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLAS 353 GYSFNLDG+++Y S+A +F+AQ++G+DLS QQ+ ++L LM+TSKG AGV G F+VL + Sbjct: 307 GYSFNLDGSTLYQSIAAIFIAQLYGIDLSWSQQLLLVLTLMVTSKGIAGVPGVSFVVLLA 366 Query: 354 TLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAK 406 TL ++ IPLEGLA + GVDR M R +N++GN +A +++A+ E +D K Sbjct: 367 TLGSVG-IPLEGLAFIAGVDRIMDMARTALNVVGNALAALVIARWEGMYDAVK 418 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: 512 Number of extensions: 24 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: 442 Length adjustment: 32 Effective length of query: 389 Effective length of database: 410 Effective search space: 159490 Effective search space used: 159490 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