Align Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter (characterized)
to candidate N515DRAFT_0019 N515DRAFT_0019 Na+/H+-dicarboxylate symporter
Query= SwissProt::O59010 (425 letters) >FitnessBrowser__Dyella79:N515DRAFT_0019 Length = 438 Score = 203 bits (516), Expect = 1e-56 Identities = 147/437 (33%), Positives = 227/437 (51%), Gaps = 57/437 (13%) Query: 12 VLQKILIGLILGAIVGLILGHY---------GYADAVKTYVKPFGDLFVRLLKMLVMPIV 62 +LQ +LIG++ AI L +G + +A AV + P G +F+RLL +V+P+V Sbjct: 11 ILQGLLIGVV-AAIATLAIGQFHPATLKTMQAFATAV---LDPLGQVFLRLLFFVVIPLV 66 Query: 63 FASLVVGAASISPARLGRVGVKIVVYYLLTSA---FAVTLGIIMARLFNPG--------- 110 FASL G A + RLGR+G + L +A AV +G++M L PG Sbjct: 67 FASLASGVAQLG--RLGRLGPLAARTFALFAANMLIAVAIGLLMMNLLQPGHQLEPGSRE 124 Query: 111 -------AGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGAL------ANGQVLPTIFF 157 G H A+ +Q QP + L + +P N GA A G VLP I F Sbjct: 125 RLLQEYGGGAHRAMERRQQQPDMS--LATAVDMFMPRNLLGAFVGHDRGALGDVLPLILF 182 Query: 158 AIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVM 217 AI++G A T L + K++ + L + + G IV ++ AP+ V A+I V+ Sbjct: 183 AILVGAAATLLDEDKRLKLQSGLDLLSELMTG-------IVGFALRLAPVAVPAMIYSVI 235 Query: 218 AEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGI-DPISFIKKAKDAMLTAFVTR 276 + G V+ L+ TA + L L + + L++ P+++ ++ + ++TAF T Sbjct: 236 VKIGTGVLLTLSVFTAGCALALALHLFGSLSLWLRLLARRSPLAYFRQIRPVLITAFSTS 295 Query: 277 SSSGTLPVTMRVAK-EMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTV 335 SSS TLP ++ +A+ E+ + F LPLGAT+NM GTAL++G F+A A G LT+ Sbjct: 296 SSSATLPASLALARDELRLRPSTAGFVLPLGATMNMSGTALFEGCVVLFVAQAFGVDLTL 355 Query: 336 GQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDM 395 GQQ ++L AVL+++ AG+PG ++A +L + G+P ++LG+D ILDM Sbjct: 356 GQQCVLMLLAVLSAVAVAGIPGGSLPLIAGLLATFGVP------PEGIGLVLGVDRILDM 409 Query: 396 GRTMVNVTGDLTGTAIV 412 RT VNV DL +V Sbjct: 410 LRTTVNVGSDLVTATVV 426 Lambda K H 0.325 0.141 0.396 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: 436 Number of extensions: 24 Number of successful extensions: 6 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: 425 Length of database: 438 Length adjustment: 32 Effective length of query: 393 Effective length of database: 406 Effective search space: 159558 Effective search space used: 159558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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