Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate H281DRAFT_01718 H281DRAFT_01718 aerobic C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_01718 Length = 452 Score = 478 bits (1229), Expect = e-139 Identities = 223/407 (54%), Positives = 314/407 (77%) Query: 9 LYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMK 68 LY QVL I GILLGHFYP++G Q+KPLGD F+KLI+M++AP+IF +VV GIA M + Sbjct: 13 LYLQVLIGIIAGILLGHFYPDVGSQLKPLGDLFIKLIRMLLAPIIFASVVVGIARMNDLH 72 Query: 69 AVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQG 128 GR G ALLYFE+ STIAL++G+++VNV +PGAGMNVDP+ +D A++ Y A+ G Sbjct: 73 EAGRVGVKALLYFEVASTIALLVGMVVVNVFKPGAGMNVDPSHIDGSAISTYTTAARQHG 132 Query: 129 IVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGI 188 ++ F ++P S++GAFA+G +L ++ F++L +L RLG + ++++ F Q +FG+ Sbjct: 133 MLDFFTSIVPNSIVGAFANGEMLPIIFFSLLLAISLARLGPRTAPFVDMLDMFLQGMFGV 192 Query: 189 INMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATGFS 248 + ++M +APIGAFG MAFTI KYG+GTL GQL++C Y+T I FVV+VLG + + G S Sbjct: 193 VRIVMYVAPIGAFGGMAFTIAKYGIGTLASFGQLMLCLYLTSIFFVVVVLGLVMRMCGLS 252 Query: 249 IFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTSIY 308 +FK++RYI++E+LI LGT+S+E+ LP+ML KME++GC + VVG+V+PTGY+FN DGT+IY Sbjct: 253 LFKYLRYIKDEILITLGTASTEAVLPQMLVKMERMGCSRPVVGMVLPTGYTFNADGTAIY 312 Query: 309 LTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAG 368 LTMAA+FIAQA N + I Q+ +L VLLL+SKG+AGV G+GF+ LAATL+++ +PV G Sbjct: 313 LTMAALFIAQAMNVHLTIWDQLLVLGVLLLTSKGSAGVAGAGFVALAATLASMHKIPVEG 372 Query: 369 LALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 L L+LG+DRF++EARA+TNL+GNGVAT+VVA+W +LD VLN Sbjct: 373 LVLLLGVDRFLNEARAVTNLIGNGVATVVVARWEGQLDMNTARAVLN 419 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: 548 Number of extensions: 21 Number of successful extensions: 1 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: 452 Length adjustment: 32 Effective length of query: 396 Effective length of database: 420 Effective search space: 166320 Effective search space used: 166320 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: 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