Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate 6936881 Sama_1055 sodium:dicarboxylate symporter (RefSeq)
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__SB2B:6936881 Length = 417 Score = 235 bits (600), Expect = 2e-66 Identities = 131/400 (32%), Positives = 212/400 (53%), Gaps = 12/400 (3%) Query: 12 QVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMKAVG 71 +VL A+GIL G E +KPLGD F+ IKM++AP++ C +V I + S + Sbjct: 14 KVLAGFALGILTGVLLGESATVLKPLGDLFIAAIKMLVAPLVLCAIVVSITSLGSSSNLK 73 Query: 72 RTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQGIVA 131 R L F + T+A +IGL + + G M + + + V G Sbjct: 74 RLSFKTLALFMLTGTLASLIGLAVGSSFDMGGSMQLASTEVRERVVP---------GFAQ 124 Query: 132 FIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGIINM 191 ++D+IP + + +G +LQ+++FA L G A++ +G K + + V ++ ++V+F + M Sbjct: 125 VLLDMIPVNPFASLTNGKVLQIIVFAALVGIAINAVGEKAEPLKKVFDAGAEVMFQLTRM 184 Query: 192 IMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAK-ATGFSIF 250 +++L PIG FG MA+ +G+YG+ TL+ LG+ II Y+ ++ +V V G + K A S Sbjct: 185 VLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIIAIYVAALIHIVFVYGGLVKFAARLSPL 244 Query: 251 KFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT-SIYL 309 +F R L+ T+SS LP E +G K V+P G + N+DG IY Sbjct: 245 QFFRKAMPAQLVAFSTASSFGTLPVTTKCAESMGVSKRYSAFVLPMGATMNMDGCGGIYP 304 Query: 310 TMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGL 369 +AA+FIAQ +D+ + + + ++S G AGV GS ++L TL VG LP+ G+ Sbjct: 305 AIAAIFIAQIYGIPLDMTDYMLIAVTATVASVGTAGVPGSAMVMLTVTLGVVG-LPLEGI 363 Query: 370 ALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKK 409 A I IDR + R TN+ G+ + +VV ELD ++ Sbjct: 364 AFIAAIDRVIDMIRTCTNVTGDMMTAVVVGNSEGELDRER 403 Lambda K H 0.327 0.142 0.401 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: 418 Number of extensions: 18 Number of successful extensions: 5 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: 428 Length of database: 417 Length adjustment: 32 Effective length of query: 396 Effective length of database: 385 Effective search space: 152460 Effective search space used: 152460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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