Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate BPHYT_RS13510 BPHYT_RS13510 C4-dicarboxylate transporter
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS13510 Length = 416 Score = 501 bits (1290), Expect = e-146 Identities = 254/414 (61%), Positives = 319/414 (77%), Gaps = 1/414 (0%) Query: 15 KKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGI 74 +KP Y LYVQV+VAI G+ LGHF P +KPLGDAFIKLV+MII+PVIF TV TGI Sbjct: 3 RKPLYKVLYVQVIVAIIIGVALGHFLPADAVAMKPLGDAFIKLVRMIISPVIFCTVVTGI 62 Query: 75 AGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFA 134 A M D++KVGRV GKA+LYF STLAL IGL+ A+V++PG G N+DP++LD A+A++A Sbjct: 63 ASMHDMRKVGRVGGKALLYFEVVSTLALAIGLLAAHVLKPGIGFNVDPSTLDAGAIASYA 122 Query: 135 AKA-HEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNS 193 A+A H + + GF +IIP T GAF GDIL VL ++LFG ALA++GE + ++ ++ Sbjct: 123 AQAAHGEGLAGFFMHIIPDTFAGAFTQGDILPVLLIAMLFGTALAVLGEPAKPLIGLIDL 182 Query: 194 LTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGA 253 L+ F++V ++ APIGAFGA+AFTIGKYG+ S+ + LIGTFY+T+ LFV LG Sbjct: 183 LSKTFFRIVRMITSLAPIGAFGAIAFTIGKYGIVSLLPMMKLIGTFYLTAFLFVSCGLGL 242 Query: 254 VARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSF 313 +AR GFS+ + YIK+ELL+VLGTS+SEAALP LM K+E+ GC R +VGLV+PTGYSF Sbjct: 243 IARACGFSLWRFVVYIKDELLIVLGTSTSEAALPQLMEKLERLGCSRGIVGLVVPTGYSF 302 Query: 314 NLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSV 373 NLDGTNIYMTLA LF+AQAT HL+ +I LL V ML+SKG+ G+TGAGFITLAA+LSV Sbjct: 303 NLDGTNIYMTLAVLFLAQATNTHLTIAQEITLLAVTMLTSKGSTGVTGAGFITLAASLSV 362 Query: 374 VPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAAL 427 VP+VPV M LILGIDRFMSECRALTN +GN VA+IV+A WE ELD +L AAL Sbjct: 363 VPTVPVTAMVLILGIDRFMSECRALTNTMGNGVASIVIAAWEKELDRGKLNAAL 416 Lambda K H 0.324 0.139 0.393 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: 588 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: 444 Length of database: 416 Length adjustment: 32 Effective length of query: 412 Effective length of database: 384 Effective search space: 158208 Effective search space used: 158208 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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