Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate BWI76_RS19175 BWI76_RS19175 dicarboxylate/amino acid:cation symporter
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Koxy:BWI76_RS19175 Length = 424 Score = 273 bits (699), Expect = 6e-78 Identities = 143/411 (34%), Positives = 247/411 (60%), Gaps = 20/411 (4%) Query: 7 LTVQVITAVIIGVIVGLV------------WPDVGKEMKPLGDTFINAVKMVIAPIIFFT 54 LT+ ++ +++G++ G W + + L D F+ +KMVIAP++F T Sbjct: 7 LTLFIVIFMLLGILSGAAIHAYAGQTTITAWSE---NITLLTDVFLRLIKMVIAPLVFST 63 Query: 55 IVLGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVS 114 + +GI ++G+ +G+VGGKA ++F + L++++GL +V + PGAGL+ + + K V Sbjct: 64 LTVGIMRLGETATIGRVGGKAMVWFITSSILSILVGLVIVTLEHPGAGLNLA-IPKESVD 122 Query: 115 QYTQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKS-VID 173 T G+ F+TH +P+++ +A A +ILQ++ FS+ FG+ A+LGEK + ++ Sbjct: 123 --TGLAVSGMSLKGFLTHTIPTSITEAMASNEILQIVVFSMFFGIAGASLGEKFNAPLVA 180 Query: 174 FFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFV 233 + VSH+ K+ GY+M AP+ F A++ I GL + AS + Y+ + L V Sbjct: 181 ALNVVSHIMLKVTGYVMYVAPLAIFAAISSVIASQGLGILLNYASFIGGYYVAILLTSAV 240 Query: 234 ALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGLVIPT 293 L + + ++ L +KD +L+ TSSSE+ P+ ++++ +GCS+++ V+P Sbjct: 241 LLAVGYMVLKKEVFRLLNMLKDPVLVAFTTSSSEAAYPKTLERLVEFGCSRNIASFVLPI 300 Query: 294 GYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLAS 353 GYSFNL G+ +Y S A +F+AQ + V LS + ++L LML SKG AGV S +VLA+ Sbjct: 301 GYSFNLVGSMVYCSFAAMFIAQAYNVQLSFSEITVMMLTLMLASKGIAGVPRSALVVLAA 360 Query: 354 TLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDE 404 T+ + IP+ G+ LL+G+D F+ GR+ +N++GNGIAT +++K+E + E Sbjct: 361 TIPSFN-IPVAGILLLMGIDHFLDMGRSAINVLGNGIATAMLSKNEGQLQE 410 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: 412 Number of extensions: 26 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: 421 Length of database: 424 Length adjustment: 32 Effective length of query: 389 Effective length of database: 392 Effective search space: 152488 Effective search space used: 152488 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: 50 (23.9 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