Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate GFF1853 PS417_09425 C4-dicarboxylate transporter
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__WCS417:GFF1853 Length = 437 Score = 498 bits (1283), Expect = e-145 Identities = 243/404 (60%), Positives = 315/404 (77%), Gaps = 1/404 (0%) Query: 22 LYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQ 81 LY+QVL+AIA G+L+GH +P++G LKPLGD FIKL+KMII P+IF TV +GI M D++ Sbjct: 10 LYIQVLIAIALGVLIGHQWPQIGIDLKPLGDGFIKLIKMIIGPIIFCTVVSGITSMHDVK 69 Query: 82 KVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKA-HEQ 140 +VGRV GKA+LYF ST+AL+IG++ A+++ PG G NID +LD +A+A F +A H + Sbjct: 70 QVGRVGGKALLYFEVVSTIALLIGILAAHLLHPGVGFNIDVKTLDSSAIAGFVGQAEHGE 129 Query: 141 SIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSLTAPVFK 200 I GFL ++IP T AF+ G+IL VLF SVLFG+ L MVGEKG +V +N + F+ Sbjct: 130 GITGFLLHVIPATFFDAFSKGEILPVLFVSVLFGVGLVMVGEKGRPLVGVINQASEVFFR 189 Query: 201 LVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGAVARYNGF 260 +V I+ + APIGAFGA+AFTIGKYGVGS+ L L+GTFY+T+ F+ +VLG++ARY GF Sbjct: 190 IVGIISRVAPIGAFGAIAFTIGKYGVGSLLPLLKLVGTFYVTAFFFIAVVLGSIARYAGF 249 Query: 261 SIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFNLDGTNI 320 SI L+ YIK ELL+VLGTSSSE+ALP L+ K+E G + VVG+V+PTGY+FNLDGTNI Sbjct: 250 SIFKLMGYIKSELLIVLGTSSSESALPQLIQKLESLGASKGVVGIVVPTGYTFNLDGTNI 309 Query: 321 YMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVVPSVPVA 380 YMTLA LF+AQAT IHL Q+ LL VAML+SKGA + GAGF+ LAA+L+VVP+VPVA Sbjct: 310 YMTLAVLFLAQATNIHLPLEQQLTLLAVAMLTSKGAGAVVGAGFVALAASLAVVPTVPVA 369 Query: 381 GMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLA 424 M LILG+DRFM+ECR+LTN++GNAVA +VVA WE ELD ++A Sbjct: 370 AMVLILGVDRFMAECRSLTNIIGNAVAALVVAAWEGELDREKMA 413 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: 668 Number of extensions: 29 Number of successful extensions: 2 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: 437 Length adjustment: 32 Effective length of query: 412 Effective length of database: 405 Effective search space: 166860 Effective search space used: 166860 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