Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate CA265_RS10595 CA265_RS10595 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__Pedo557:CA265_RS10595 Length = 458 Score = 283 bits (725), Expect = 6e-81 Identities = 148/374 (39%), Positives = 235/374 (62%), Gaps = 15/374 (4%) Query: 50 LGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVA 109 L D F++L+KMI+AP++F T+ G+A + D++ VGR+ GK + +FL S ++L++G+++ Sbjct: 92 LSDIFLRLIKMIVAPLVFTTLVVGVAKVGDIKAVGRIGGKTLGWFLAMSLMSLVLGMVLV 151 Query: 110 NVVQPGAGMNIDPASLDPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFF 169 N+ +PG M + SL V T KA S+ F+ ++ P +I + + +ILQ++ F Sbjct: 152 NLFEPGRHMKL---SLPDQLVNTGIQKA-AMSVKDFIAHVFPKSIAESMSTNEILQIVVF 207 Query: 170 SVLFGIALAMVGEKGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSI 229 S+ FG+A A +G+ G+ V+ +++ + K+ +M AP+ FGAM + K G+ + Sbjct: 208 SLFFGVATAAIGDLGQIVIKAFDAIAHVILKMTGYVMNFAPLAVFGAMTAIVAKQGLNVL 267 Query: 230 ANLAMLIGTFYITSLLFVFIVLGAVARYNGFSIVA-----LLRYIKEELLLVLGTSSSEA 284 A+ IG FY+ +L AV + GF ++ L+ +KE LL T+SSEA Sbjct: 268 NTYAIFIGEFYLG-----LAILWAVLIFLGFLVLKKRIFRLVNDMKEPALLAFSTASSEA 322 Query: 285 ALPGLMNKMEKAGCKRSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQIL 344 A P M +E+ GCK +V V+P GYSFNLDG+ +YMT A+LFIAQA GIHL + QI Sbjct: 323 AYPKTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYMTFASLFIAQAYGIHLGFEQQIS 382 Query: 345 LLLVAMLSSKGAAGITGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGN 404 +LL+ ML+SKG AG+ A + +A T++ ++P AG+AL++GID + R+ TN+VGN Sbjct: 383 MLLILMLTSKGIAGVPRASLVVIAGTIASF-NIPEAGLALLIGIDPLLDMGRSATNVVGN 441 Query: 405 AVATIVVARWENEL 418 ++AT VV++WE EL Sbjct: 442 SIATAVVSKWEGEL 455 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: 475 Number of extensions: 24 Number of successful extensions: 4 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: 458 Length adjustment: 33 Effective length of query: 411 Effective length of database: 425 Effective search space: 174675 Effective search space used: 174675 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