Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate CCNA_01161 CCNA_01161 proton/sodium-glutamate symport protein
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__Caulo:CCNA_01161 Length = 448 Score = 226 bits (576), Expect = 1e-63 Identities = 149/451 (33%), Positives = 230/451 (50%), Gaps = 22/451 (4%) Query: 1 MAAAQSSKI----GLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFI 56 MAA Q+ G ++LI M AG+ +GLL R G +E Y+ +G IF+ Sbjct: 1 MAATQTKSSRFISGFGAQVLIAMVAGLGLGLLARQL-GPAEGQAGYVLAETLRQVGQIFV 59 Query: 57 NSLKMLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG 116 L++LV PLVF ++V ++++ RL +TL ++ T I++V+ I+ +++QPG Sbjct: 60 QLLRVLVPPLVFTAIVASIANIAQMQNAARLVWRTLFWFAVTALISVVIGIALGLVLQPG 119 Query: 117 NASLASESMQYSAKEAPSLADVLINIVPSNPM------KALSEG--------NMLQIIIF 162 + + + K S D L +VP N + K G N+LQI++ Sbjct: 120 LHASLDAAAAKAPKTHGSWLDFLTGLVPVNILGLAASTKISDAGAASTSLSFNVLQIVVI 179 Query: 163 AVIFGFAISHIGERGRRVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETL 222 +++ G A +GE G ++ +V+ +++L P G L G G TL Sbjct: 180 SLVTGVAALKVGEAGEAFLKFNASALAIVRKVLWWVIRLTPIGTVGLFGNAVAQYGWTTL 239 Query: 223 ESVIKYFMLVLVVLLFHGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPV 282 + + + + L VVYP LL L + L+P+ F + AF + SS TLPV Sbjct: 240 GQLGAFTVAIYAGLGLVLLVVYPVLLAL-NDLNPIRFFQGAWPAIQLAFVSRSSIGTLPV 298 Query: 283 TMEASEHRLGADNKVASFTLPLGATINMDG-TAIMQGVATVFIAQVFGIDLTITDYAMVV 341 T +E RLG A+F +PLGAT MDG AI +A +F+AQ FG+ L +DY ++V Sbjct: 299 TETVTETRLGVPRAYAAFAVPLGATTKMDGCAAIYPAIAAIFVAQFFGVHLVWSDYLLIV 358 Query: 342 MTATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVA 401 + + S TAG+ G VML + L+ +GLP+EG L+L +D +LDM RTAVNV G + Sbjct: 359 FVSVIGSAATAGLTGA-TVMLTLTLSTLGLPLEGAGLLLAIDPILDMGRTAVNVAGQALV 417 Query: 402 TVVIAKSEGALNEAVFNDPKAGKTAGSFDAE 432 ++AK EG L+ +N P + A AE Sbjct: 418 PTLVAKREGILDLEAYNRPGSHADAAFHAAE 448 Lambda K H 0.325 0.139 0.388 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: 410 Number of extensions: 19 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: 437 Length of database: 448 Length adjustment: 32 Effective length of query: 405 Effective length of database: 416 Effective search space: 168480 Effective search space used: 168480 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