Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Ac3H11_719 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_719 Length = 456 Score = 504 bits (1297), Expect = e-147 Identities = 239/415 (57%), Positives = 323/415 (77%) Query: 1 MKTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTG 60 ++ ++ LYFQV+ AI +G+LLGHF P GE +KPLGD F+KL+KMIIAPVIF T+VTG Sbjct: 12 VRLPFYRQLYFQVVLAIVLGVLLGHFEPSYGEALKPLGDAFIKLVKMIIAPVIFLTIVTG 71 Query: 61 IAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVY 120 IAGM + VGR A+ YF ST+AL++GL++ NVVQPGAGMN++ A LD AV Y Sbjct: 72 IAGMSQLSTVGRVFGKAMAYFLFFSTLALVVGLVVANVVQPGAGMNINVADLDQSAVKGY 131 Query: 121 ADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIES 180 ++ + + F +D+IP +++ F NILQVLL AVLFG L +G G+ + N +++ Sbjct: 132 VAKSHEMTLTGFALDIIPKTLVSPFVGDNILQVLLVAVLFGVGLAMVGDAGRPVLNFLDA 191 Query: 181 FSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGS 240 + +F ++ ++M+ AP+GAFGAMAFTIGK+G+G+LV L L+ FYIT +LFVV++LG Sbjct: 192 LTTPVFKVVGIVMKAAPLGAFGAMAFTIGKFGLGSLVNLAWLVGSFYITSLLFVVVILGF 251 Query: 241 IAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSF 300 +A+ GFS+FK RY++ EL++VLGTSSSESALP +++KMEK GC KSVVGLV+PTGYSF Sbjct: 252 VARLCGFSVFKLCRYLKAELMLVLGTSSSESALPSLMEKMEKAGCSKSVVGLVVPTGYSF 311 Query: 301 NLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSA 360 NLDGT+IY+T+AA+FIAQATN+++ + HQ+ LL+V +LSSKGAAGVTG+GFI LAATL+ Sbjct: 312 NLDGTNIYMTLAALFIAQATNTELTLGHQVALLLVAMLSSKGAAGVTGAGFITLAATLAV 371 Query: 361 VGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 V +PVAG+ALILG+DRFMSE R+LTN +GN VAT+VV++W LDH++LD LN Sbjct: 372 VPEVPVAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWENALDHERLDAALN 426 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: 625 Number of extensions: 25 Number of successful extensions: 1 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: 456 Length adjustment: 32 Effective length of query: 396 Effective length of database: 424 Effective search space: 167904 Effective search space used: 167904 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: 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