Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate BPHYT_RS13510 BPHYT_RS13510 C4-dicarboxylate transporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__BFirm:BPHYT_RS13510 Length = 416 Score = 480 bits (1235), Expect = e-140 Identities = 243/411 (59%), Positives = 315/411 (76%), Gaps = 1/411 (0%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 L+K LY QV+ AI IG+ LGHF P MKPLGD F+KL++MII+PVIFCTVVTGIA M Sbjct: 6 LYKVLYVQVIVAIIIGVALGHFLPADAVAMKPLGDAFIKLVRMIISPVIFCTVVTGIASM 65 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 M+ VGR G ALLYFE+VST+AL IGL+ +V++PG G NVDP+TLDA A+A YA QA Sbjct: 66 HDMRKVGRVGGKALLYFEVVSTLALAIGLLAAHVLKPGIGFNVDPSTLDAGAIASYAAQA 125 Query: 125 KD-QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQ 183 +G+ F M +IP + GAF G+IL VLL A+LFG AL LG + + +I+ S+ Sbjct: 126 AHGEGLAGFFMHIIPDTFAGAFTQGDILPVLLIAMLFGTALAVLGEPAKPLIGLIDLLSK 185 Query: 184 VIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAK 243 F I+ MI LAPIGAFGA+AFTIGKYG+ +L+ + +LI FY+T LFV LG IA+ Sbjct: 186 TFFRIVRMITSLAPIGAFGAIAFTIGKYGIVSLLPMMKLIGTFYLTAFLFVSCGLGLIAR 245 Query: 244 ATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLD 303 A GFS+++F+ YI++ELLIVLGTS+SE+ALP++++K+E+LGC + +VGLV+PTGYSFNLD Sbjct: 246 ACGFSLWRFVVYIKDELLIVLGTSTSEAALPQLMEKLERLGCSRGIVGLVVPTGYSFNLD 305 Query: 304 GTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGH 363 GT+IY+T+A +F+AQATN+ + I +ITLL V +L+SKG+ GVTG+GFI LAA+LS V Sbjct: 306 GTNIYMTLAVLFLAQATNTHLTIAQEITLLAVTMLTSKGSTGVTGAGFITLAASLSVVPT 365 Query: 364 LPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVL 414 +PV + LILGIDRFMSE RALTN +GNGVA+IV+A W KELD KL+ L Sbjct: 366 VPVTAMVLILGIDRFMSECRALTNTMGNGVASIVIAAWEKELDRGKLNAAL 416 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: 523 Number of extensions: 23 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: 416 Length adjustment: 32 Effective length of query: 396 Effective length of database: 384 Effective search space: 152064 Effective search space used: 152064 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