Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate BPHYT_RS16825 BPHYT_RS16825 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__BFirm:BPHYT_RS16825 Length = 441 Score = 433 bits (1114), Expect = e-126 Identities = 211/411 (51%), Positives = 305/411 (74%), Gaps = 1/411 (0%) Query: 6 FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 F SL+ +V+ A+ GI++G +P + ++PLGDGF+KLIKM+I P++FC VV+G+A Sbjct: 5 FNSLFGRVVIALVAGIVVGAVFPHFAQSLRPLGDGFLKLIKMVIGPIVFCVVVSGMAHAG 64 Query: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125 ++ VGR G A++YFE+++TIAL+IG I+ V +PG GMN+D +LD +++ Y + AK Sbjct: 65 DLRKVGRVGLKAVIYFEVMTTIALVIGAILAYVTRPGVGMNIDLHSLDPASLSTYTEHAK 124 Query: 126 D-QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 + F++ +IP + I AFA+G+ILQ+L+F+VLFG AL LG+K Q + ++I+ SQV Sbjct: 125 SLKDTAGFLLKIIPDTAINAFATGDILQILVFSVLFGSALSLLGNKAQRVSSLIDELSQV 184 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 F ++ I++LAP+G GA+AFT G YGV +L QLG L++ FY++C +FVV+VLG + + Sbjct: 185 FFRVMGFIIKLAPLGVLGAIAFTTGTYGVESLKQLGMLVLVFYLSCFVFVVVVLGVVMRL 244 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 GFSIFK IRY+REEL IVLGT+SS++ LP+++ K+E +G + S VGLVIPTGYSFNLDG Sbjct: 245 AGFSIFKLIRYLREELSIVLGTASSDAVLPQIMRKLEWMGVKDSTVGLVIPTGYSFNLDG 304 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 SIYLT+A +FIAQATN+ + + I +++V L++SKGA G+ GS ++LAATLSA+ + Sbjct: 305 FSIYLTLAVIFIAQATNTPLSVHDLIVVVLVSLVTSKGAHGIPGSAIVILAATLSAIPAI 364 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 PV GL LIL +D F+ ARALTNL+GN VAT+VVA W ++D + VLN Sbjct: 365 PVLGLVLILPVDWFVGIARALTNLIGNCVATVVVAVWENDIDRARAHRVLN 415 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: 582 Number of extensions: 37 Number of successful extensions: 3 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: 441 Length adjustment: 32 Effective length of query: 396 Effective length of database: 409 Effective search space: 161964 Effective search space used: 161964 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