Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate BPHYT_RS33330 BPHYT_RS33330 C4-dicarboxylate ABC transporter
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__BFirm:BPHYT_RS33330 Length = 435 Score = 210 bits (534), Expect = 8e-59 Identities = 137/413 (33%), Positives = 224/413 (54%), Gaps = 26/413 (6%) Query: 11 LTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFIS 70 LT I+ GM G+++G + G+ + G+F +I IF+ +KM++ PLVF + Sbjct: 5 LTFYIVAGMALGVIVGYVCHRSAAGA--AEAKTIAGYFSIITDIFLRLVKMIIAPLVFAT 62 Query: 71 LVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG---NASLASESMQY 127 LV G + S + R+G +++ +++ + +L + ++ A +QPG + + S + Sbjct: 63 LVSGLAGMEGTSDVRRIGFRSVGWFVCASLFSLALGLALANALQPGAGLHMTQTSSDVAT 122 Query: 128 SAKEAP-SLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALF-- 184 A + D + + PS+ + A++ ++LQI++F+V+FG +S I ++ RV L Sbjct: 123 GLNTAGLNFKDFVTHAFPSSIIDAMARNDILQILVFSVLFGVVLSAI-KKDPRVTPLIAG 181 Query: 185 -DDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIK-----YFMLVL--VVL 236 D L ++++ +M+LAP GVF + G++ L + K Y LV +VL Sbjct: 182 IDALVPAMLKLTDYVMRLAPIGVFGALASAITVNGLDVLTTYGKLVGSFYLGLVTLWIVL 241 Query: 237 LFHGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNK 296 +F G+ F G S ++ +R+ + AFSTASS A P E E G D K Sbjct: 242 IFVGYA--------FLGKSIWRLLKAVREPAMLAFSTASSEAAYPRLTEKLE-AFGIDKK 292 Query: 297 VASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPG 356 V FTLPLG N+DG+ + Q A +FIAQ FGID+ + M+++ L+S G AGV Sbjct: 293 VVGFTLPLGYAFNLDGSMMYQAFAAIFIAQAFGIDMPLGAQIMMLLVLMLSSKGMAGVAR 352 Query: 357 VGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSE 409 +V++A + LP G+ LIL +D++LDM RTA NV G+++AT VIAK E Sbjct: 353 GSVVVVAAIAPMFHLPPSGVVLILAIDQILDMGRTATNVIGNSIATAVIAKWE 405 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: 383 Number of extensions: 15 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: 435 Length adjustment: 32 Effective length of query: 405 Effective length of database: 403 Effective search space: 163215 Effective search space used: 163215 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