Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 7024548 Shewana3_1726 sodium:dicarboxylate symporter (RefSeq)
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__ANA3:7024548 Length = 437 Score = 706 bits (1823), Expect = 0.0 Identities = 364/437 (83%), Positives = 400/437 (91%) Query: 1 MAAAQSSKIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLK 60 MA K GLT KIL GM GI +GL+LRN F S+ V+DYITEGF HVIGTIFI+SLK Sbjct: 1 MATLLQKKFGLTSKILFGMATGIALGLILRNVFPESDIVKDYITEGFLHVIGTIFISSLK 60 Query: 61 MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASL 120 MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIAL++AI +AVLV PGNASL Sbjct: 61 MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALILAIVSAVLVHPGNASL 120 Query: 121 ASESMQYSAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRV 180 ASE M+Y+AKEAPSL+ VLINIVP+NPM+A+SEGNMLQIIIFAVIFGFAI+HIGERG+RV Sbjct: 121 ASEKMEYTAKEAPSLSSVLINIVPTNPMQAMSEGNMLQIIIFAVIFGFAIAHIGERGKRV 180 Query: 181 AALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHG 240 AALF+DLNEVIMRVVTLIMQLAPYGVFALM KLALTLG+ T ESV+KYF +VLVVLL H Sbjct: 181 AALFEDLNEVIMRVVTLIMQLAPYGVFALMAKLALTLGLGTFESVVKYFFVVLVVLLIHA 240 Query: 241 FVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASF 300 F+VYPTLLKLFSGL+PL+FIRKMRDVQLFAFSTASSNATLP+T+EASEHRLG DNK+ASF Sbjct: 241 FIVYPTLLKLFSGLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASF 300 Query: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLV 360 TLPLGATINMDGTAIMQGVATVFIAQVFGI+LTITDYA VV+TATLASIGTAGVPGVGL+ Sbjct: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIELTITDYAAVVVTATLASIGTAGVPGVGLI 360 Query: 361 MLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFNDP 420 MLAMVLNQVGLPVEGIALI+GVDR+LDMVRTAVNVTGD VATVVIAKSEG NE VFN+ Sbjct: 361 MLAMVLNQVGLPVEGIALIIGVDRLLDMVRTAVNVTGDCVATVVIAKSEGEFNETVFNNT 420 Query: 421 KAGKTAGSFDAEVHRGE 437 +AGK A +FD +VH+ E Sbjct: 421 QAGKVASNFDEQVHKVE 437 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: 609 Number of extensions: 16 Number of successful extensions: 1 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: 437 Length adjustment: 32 Effective length of query: 405 Effective length of database: 405 Effective search space: 164025 Effective search space used: 164025 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