Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 6936881 Sama_1055 sodium:dicarboxylate symporter (RefSeq)
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__SB2B:6936881 Length = 417 Score = 300 bits (769), Expect = 4e-86 Identities = 170/412 (41%), Positives = 246/412 (59%), Gaps = 15/412 (3%) Query: 7 SKIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPL 66 +KI K+L G GIL G+LL G S V +G +FI ++KMLV PL Sbjct: 7 NKIPFWQKVLAGFALGILTGVLL----GESATV--------LKPLGDLFIAAIKMLVAPL 54 Query: 67 VFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQ 126 V ++V SL S L RL KTLA ++ T +A ++ ++ G S+ S + Sbjct: 55 VLCAIVVSITSLGSSSNLKRLSFKTLALFMLTGTLASLIGLAVGSSFDMGG-SMQLASTE 113 Query: 127 YSAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDD 186 + P A VL++++P NP +L+ G +LQII+FA + G AI+ +GE+ + +FD Sbjct: 114 VRERVVPGFAQVLLDMIPVNPFASLTNGKVLQIIVFAALVGIAINAVGEKAEPLKKVFDA 173 Query: 187 LNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPT 246 EV+ ++ ++++L P GVF LM + G+ TL + K+ + + V L H VY Sbjct: 174 GAEVMFQLTRMVLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIIAIYVAALIHIVFVYGG 233 Query: 247 LLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGA 306 L+K + LSPL F RK QL AFSTASS TLPVT + +E +G + ++F LP+GA Sbjct: 234 LVKFAARLSPLQFFRKAMPAQLVAFSTASSFGTLPVTTKCAE-SMGVSKRYSAFVLPMGA 292 Query: 307 TINMDGT-AIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMV 365 T+NMDG I +A +FIAQ++GI L +TDY ++ +TAT+AS+GTAGVPG +VML + Sbjct: 293 TMNMDGCGGIYPAIAAIFIAQIYGIPLDMTDYMLIAVTATVASVGTAGVPGSAMVMLTVT 352 Query: 366 LNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVF 417 L VGLP+EGIA I +DR++DM+RT NVTGD + VV+ SEG L+ F Sbjct: 353 LGVVGLPLEGIAFIAAIDRVIDMIRTCTNVTGDMMTAVVVGNSEGELDRERF 404 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: 394 Number of extensions: 14 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: 417 Length adjustment: 32 Effective length of query: 405 Effective length of database: 385 Effective search space: 155925 Effective search space used: 155925 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