Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate 202663 SO3562 proton/glutamate symporter, putative (NCBI ptt file)
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__MR1:202663 Length = 413 Score = 248 bits (632), Expect = 3e-70 Identities = 134/396 (33%), Positives = 217/396 (54%), Gaps = 11/396 (2%) Query: 12 QVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMKAVG 71 +VLT +G L+G E +KPLGD F+ IKM++AP++FC++V I + S + Sbjct: 14 KVLTGFILGALVGVLLGESATVLKPLGDLFISAIKMLVAPLVFCSIVVSITSLGSQTNLK 73 Query: 72 RTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQGIVA 131 R L F + TIA +IGL + +++ G M + AT + + + G Sbjct: 74 RLSIKTLGMFMLTGTIASLIGLAVGSLIDMGGTMQL--ATTEVR-------ERNIPGFAQ 124 Query: 132 FIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGIINM 191 ++D+IP + + A G +LQ+++FA L G A++++G K + + IE+ ++V+F + M Sbjct: 125 VLLDMIPINPFASLAEGKVLQIIVFAALVGIAINKVGEKAEPLKRTIEAGAEVMFQLTRM 184 Query: 192 IMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATGFSIFK 251 +++L PIG FG MA+ +G+YG+ TL+ LG+ I YI ++ ++ V G K G S + Sbjct: 185 VLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIAAIYIAALVHMIFVYGGFVKLAGLSPIQ 244 Query: 252 FIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT-SIYLT 310 F R L+ TSSS LP +E +G K V+P G + N+DG IY Sbjct: 245 FFRKALPAQLVAFSTSSSFGTLPASTRAVETMGVSKRYSAFVMPLGATMNMDGCGGIYPA 304 Query: 311 MAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLA 370 +AA+FIAQ +D + + + + ++S G AGV GS ++L TL +G LP+ G+A Sbjct: 305 IAAIFIAQIYGIPLDTLDYVMIAVTATIASVGTAGVPGSAMVMLTVTLGVIG-LPLEGIA 363 Query: 371 LILGIDRFMSEARALTNLVGNGVATIVVAKWVKELD 406 I IDR + R TN+ G+ + +V+ K ELD Sbjct: 364 FIASIDRIIDMIRTTTNVTGDMMTAVVIGKSENELD 399 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: 430 Number of extensions: 23 Number of successful extensions: 6 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: 413 Length adjustment: 32 Effective length of query: 396 Effective length of database: 381 Effective search space: 150876 Effective search space used: 150876 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