Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate CCNA_00264 CCNA_00264 C4-dicarboxylate transport protein
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Caulo:CCNA_00264 Length = 417 Score = 271 bits (693), Expect = 3e-77 Identities = 150/422 (35%), Positives = 253/422 (59%), Gaps = 22/422 (5%) Query: 9 KSLYFQVIVAIAIGILLG----HFYPQTGVA-----LKPLGDGFIKLIKMVIAPIIFCTV 59 K + +I ++ +G+L+G F G L + D F++LIKM+IAP++F T+ Sbjct: 3 KRFAYLIIASMILGVLVGWTCNQFLDPAGAKSAADNLSIITDIFLRLIKMIIAPLVFTTL 62 Query: 60 VSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGM---HIDVSTLDA 116 V+G+A M++ +VG+ G + +F S ++L++GL++V+++ PG G+ H+DV+ Sbjct: 63 VAGVAHMEDAAAVGRIGAKTMTWFIGASAVSLVLGLLMVHLLDPGAGLNMAHVDVAMKTT 122 Query: 117 SKVAAYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPV 176 + A+ ++ GFI +++P +I A A +ILQ+++FS+ G A+ L + Sbjct: 123 ATTDAF-------TLKGFITHLVPTSIFDAMAKNEILQIVVFSLFVGTAVAALDDKAPQI 175 Query: 177 LDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITC-VLF 235 L+ +++ A +M + +MKLAP+ A+A TI G+G L G+ ++ FY VL+ Sbjct: 176 LELVEQAAQIMLKVTGFVMKLAPLAIFAALASTIATQGLGMLATYGKFVLGFYSAMGVLW 235 Query: 236 VLVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLV 295 L+ + + G V+ L IR+ +L+ T+SSE+A PR+L + ++G ++ +V V Sbjct: 236 ALLFIAGLL-VLGKRVIPLFGVIRDPVLLAFSTASSEAAYPRILDSLPKVGVRRRIVSFV 294 Query: 296 IPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIV 355 +P GYSFNLDG+ +Y T A +FI QA + + QI +LL+L+++SKG AGV + +V Sbjct: 295 LPLGYSFNLDGSMLYCTFATMFIVQAHGVELTVQQQIFMLLLLMVTSKGIAGVPRASLVV 354 Query: 356 LAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAE 415 + ATL+ G LP A +AL+LG+D + R+ TN+VGN+VA VVAKW ELD+ + E Sbjct: 355 IMATLTYFG-LPEAWIALVLGVDHLLDMGRSATNVVGNSVAAAVVAKWEGELDDIPPEGE 413 Query: 416 LA 417 A Sbjct: 414 AA 415 Lambda K H 0.326 0.142 0.402 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: 449 Number of extensions: 21 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: 417 Length adjustment: 32 Effective length of query: 412 Effective length of database: 385 Effective search space: 158620 Effective search space used: 158620 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 (21.6 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