Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate AZOBR_RS28110 AZOBR_RS28110 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__azobra:AZOBR_RS28110 Length = 457 Score = 451 bits (1161), Expect = e-131 Identities = 222/412 (53%), Positives = 303/412 (73%) Query: 4 SLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAG 63 + +K+LYFQV+ + +GIL GHF+P++G +KPLGDGFVKL+KM+IAPV+FCT+V+GI Sbjct: 17 AFYKALYFQVVVGLTLGILAGHFWPDLGASLKPLGDGFVKLVKMMIAPVVFCTIVSGITS 76 Query: 64 MESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQ 123 + + +G+T ++ F ++ AL+IGL V +++PG GM+V A+LD A YA Q Sbjct: 77 LNDTREIGKTLVKSMALFYALTVAALLIGLAAVMIIEPGVGMHVSAASLDPTVAARYAKQ 136 Query: 124 AKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQ 183 A G F++ +IP S GAFA G +L VLL +VL GF L R+G G+ + IESFS Sbjct: 137 AAPVGFTDFVLHIIPHSFFGAFAEGEVLPVLLISVLVGFGLTRVGKAGEPVVQGIESFSH 196 Query: 184 VIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAK 243 V+F IM+LAPIGAFGAMAFT+GKYG+ ++ LG LI+ FY+ C +F+++V+G++A+ Sbjct: 197 VLFAAFGFIMKLAPIGAFGAMAFTVGKYGIDSIGSLGLLILTFYVACGVFLMVVIGTLAR 256 Query: 244 ATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLD 303 GFS++K +RY REELLIVLGTSSSE LPR+L K+E LGC+K V GLV+P GYSFNLD Sbjct: 257 LHGFSLWKVLRYFREELLIVLGTSSSEPVLPRVLQKLEALGCKKGVSGLVLPMGYSFNLD 316 Query: 304 GTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGH 363 GT+IYLT+A++FIAQA + + +L V+LL+SKGAAGVTGSGF+ L ATL+ + Sbjct: 317 GTAIYLTLASLFIAQACDIHLSGGQIFAMLGVMLLTSKGAAGVTGSGFVALVATLTVMPD 376 Query: 364 LPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 LPVAG+AL++GIDRFMSEARALT+++ N VA+IVV+ W D + L LN Sbjct: 377 LPVAGVALLVGIDRFMSEARALTSIISNCVASIVVSIWENACDREVLQRELN 428 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: 529 Number of extensions: 22 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: 457 Length adjustment: 32 Effective length of query: 396 Effective length of database: 425 Effective search space: 168300 Effective search space used: 168300 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