Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 5208721 Shew_1224 sodium:dicarboxylate symporter (RefSeq)
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__PV4:5208721 Length = 416 Score = 297 bits (760), Expect = 5e-85 Identities = 165/405 (40%), Positives = 245/405 (60%), Gaps = 15/405 (3%) Query: 14 KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVC 73 K+L G G+ +G++L G + Q +G +FI ++KMLV PL+F ++V Sbjct: 13 KVLAGFILGVGLGVVL-----GEQATQ-------LKPLGDLFIAAIKMLVAPLIFCAIVV 60 Query: 74 GTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQYSAKEAP 133 SL L RL KTLA ++ T IA ++ ++ L+ G SL + + + P Sbjct: 61 SITSLGNDVSLKRLSIKTLAMFMLTGTIASLIGLAIGSLIDMGG-SLELATTEVRERNVP 119 Query: 134 SLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLNEVIMR 193 A VL++++P NP +L+EG +LQII+FA + G AI+ IGE+ + + EV+ + Sbjct: 120 GFAQVLLDMIPVNPFASLAEGKVLQIIVFAALVGIAINKIGEKAEPLKRTIEAGAEVMFQ 179 Query: 194 VVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTLLKLFSG 253 + +++QL P GVF LM + G+ TL + K+ + + L H VY L++ +G Sbjct: 180 LTRMVLQLTPIGVFGLMAWVVGEYGLSTLLPLGKFIGAIYIAALIHMVFVYGGLVRFGAG 239 Query: 254 LSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATINMDGT 313 LS + F RK QL AF+TASS TLP + A+E +G K +F LPLGAT+NMDG Sbjct: 240 LSAVQFFRKAMPAQLVAFTTASSFGTLPASTRATE-TMGVSKKYGAFVLPLGATMNMDGC 298 Query: 314 A-IMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLP 372 I +A +FIAQ++GI L +TDY ++ +TAT+AS+GTAGVPG +VML++ L VGLP Sbjct: 299 GGIYPAIAAIFIAQIYGIPLEMTDYMLIAVTATVASVGTAGVPGSAMVMLSVTLGVVGLP 358 Query: 373 VEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVF 417 +EGIA I +DR++DM+RTA NVTGD + VV+ KSEG L++ F Sbjct: 359 LEGIAFIASIDRVIDMIRTATNVTGDMMTAVVVGKSEGQLDQEQF 403 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: 403 Number of extensions: 13 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: 437 Length of database: 416 Length adjustment: 32 Effective length of query: 405 Effective length of database: 384 Effective search space: 155520 Effective search space used: 155520 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