Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate BWI76_RS19175 BWI76_RS19175 dicarboxylate/amino acid:cation symporter
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__Koxy:BWI76_RS19175 Length = 424 Score = 272 bits (696), Expect = 1e-77 Identities = 151/405 (37%), Positives = 245/405 (60%), Gaps = 14/405 (3%) Query: 12 ILFAMVLGILLGSYLHYHSDSRDWLV----VNLLSPAGDIFIHLIKMIVVPIVISTLVVG 67 I+ M+LGIL G+ +H ++ + LL+ D+F+ LIKM++ P+V STL VG Sbjct: 11 IVIFMLLGILSGAAIHAYAGQTTITAWSENITLLT---DVFLRLIKMVIAPLVFSTLTVG 67 Query: 68 IAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKYQS 127 I +G+ +GR+G K +++F + ++I++G+ + + PGAG++++ I K +S Sbjct: 68 IMRLGETATIGRVGGKAMVWFITSSILSILVGLVIVTLEHPGAGLNLA------IPK-ES 120 Query: 128 TTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREPLVT 187 + S + G + +PT+I +MA E+L I+ FS+ FG+ +SL PLV Sbjct: 121 VDTGLAVSGMSLKGFLTHTIPTSITEAMASNEILQIVVFSMFFGIAGASLGEKFNAPLVA 180 Query: 188 VFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFFALV 247 +S M KVT VM AP+ +FA I+ +A+ G L A + + AIL + V Sbjct: 181 ALNVVSHIMLKVTGYVMYVAPLAIFAAISSVIASQGLGILLNYASFIGGYYVAILLTSAV 240 Query: 248 VLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFVVPT 307 +L + + V+ L+ +LKD +++A++T+SSE+ P+ +E++ +G +I SFV+P Sbjct: 241 LLAVGYMVLKKEVFRLLNMLKDPVLVAFTTSSSEAAYPKTLERLVEFGCSRNIASFVLPI 300 Query: 308 GYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVVLLA 367 GYSFNL GS +Y S AA+FIAQ Y + LS + +++LTLM+ SKGIAGVP + VVL A Sbjct: 301 GYSFNLVGSMVYCSFAAMFIAQAYNVQLSFSEITVMMLTLMLASKGIAGVPRSALVVLAA 360 Query: 368 TLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWE 412 T+ S IP+ G+ + G+D LDM R+A+NV+GN +A +++K E Sbjct: 361 TIPSFNIPVAGILLLMGIDHFLDMGRSAINVLGNGIATAMLSKNE 405 Lambda K H 0.326 0.141 0.403 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: 431 Number of extensions: 20 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: 437 Length of database: 424 Length adjustment: 32 Effective length of query: 405 Effective length of database: 392 Effective search space: 158760 Effective search space used: 158760 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 (21.7 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