Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate H281DRAFT_02039 H281DRAFT_02039 aerobic C4-dicarboxylate transport protein
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__Burk376:H281DRAFT_02039 Length = 443 Score = 548 bits (1412), Expect = e-160 Identities = 272/424 (64%), Positives = 338/424 (79%) Query: 6 LDAVAGSKGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPV 65 L +AG+ KKP + LYVQV+VAI GI LGH+YP L +KPLGD FIKL+KM+I P+ Sbjct: 10 LTHIAGTIVKKPIHKVLYVQVIVAIIIGIALGHYYPNLAVDMKPLGDGFIKLIKMVIGPI 69 Query: 66 IFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASL 125 IF TV TGIAGM D++KVGRV GKA+LYF ST AL++GLI +V++PG G NIDPA+L Sbjct: 70 IFCTVVTGIAGMEDMKKVGRVGGKALLYFEIVSTFALVLGLIATHVLKPGVGFNIDPATL 129 Query: 126 DPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGE 185 D AVA++AAKAH Q+ V FL ++IP T+V AFA G+ILQ+L ++LFG LA GE+G+ Sbjct: 130 DGKAVASYAAKAHGQTTVDFLMHLIPDTLVSAFAQGEILQILLIALLFGAVLATAGERGK 189 Query: 186 QVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLL 245 V NF+ L+ +F +V I+ K APIGAFGAMAFTIGKYG+GS+ + LIGTFY+TS++ Sbjct: 190 VVTNFIEGLSHVLFGIVRIITKLAPIGAFGAMAFTIGKYGIGSLLPMLKLIGTFYLTSIV 249 Query: 246 FVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGL 305 FV +VLG +AR GF+I+ + YIKEE+L+VLGTSSSEAALP LM K+E GC RSVVGL Sbjct: 250 FVVVVLGIIARAVGFNILRFIAYIKEEMLIVLGTSSSEAALPQLMLKLENLGCSRSVVGL 309 Query: 306 VIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFI 365 V+PTGYSFNLDGTNIYMT+A LFIAQAT L+W Q+ LL V ML+SKGA+G+TGAGFI Sbjct: 310 VVPTGYSFNLDGTNIYMTMAVLFIAQATNTDLTWAQQLTLLAVTMLTSKGASGVTGAGFI 369 Query: 366 TLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAA 425 TLAATL+VVP++P++GM LILGIDRFMSECRALTN+VGN VAT+VV+ WE ELD +L + Sbjct: 370 TLAATLAVVPTIPLSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNKLNS 429 Query: 426 ALGG 429 AL G Sbjct: 430 ALRG 433 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: 646 Number of extensions: 33 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: 443 Length adjustment: 32 Effective length of query: 412 Effective length of database: 411 Effective search space: 169332 Effective search space used: 169332 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