Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate CA265_RS15560 CA265_RS15560 glutamate/aspartate:proton symporter GltP
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Pedo557:CA265_RS15560 Length = 428 Score = 437 bits (1125), Expect = e-127 Identities = 217/405 (53%), Positives = 303/405 (74%), Gaps = 2/405 (0%) Query: 7 LYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGM 66 ++ +L FQV++AI IGI +G ++P K + GFI LI M+IAPIIF T+V GIA M Sbjct: 10 VFSNLTFQVLLAIIIGIYVGAYFPGFAPTAKLISQGFINLISMLIAPIIFFTIVLGIAHM 69 Query: 67 QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAG 126 +MK VG+ GG ALLYFEIVST+A+ IGL+V NV++PG GM DA+K+A Y Sbjct: 70 GDMKKVGRVGGKALLYFEIVSTVAIAIGLLVANVLKPGAGMIAKAG--DATKIAGYAEQA 127 Query: 127 KDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186 KD + F L++IP+ I+ +FA G+ILQ+L+F+++FG+ L++LG G VL+ D+ + V Sbjct: 128 KDMNWAEFFLHIIPHNIIASFAEGNILQILLFAILFGYGLNKLGGEGTTVLNAFDKISKV 187 Query: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRA 246 +F I+ +IM+LAPIGA G MAF+IG +G+ S+V + +LM Y+TC LF+ V+L ICR Sbjct: 188 LFKIMKLIMRLAPIGAFGGMAFSIGTHGLESIVGMAKLMGSVYLTCFLFIFVILNGICRY 247 Query: 247 HGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306 + FS+ ++YIR+E+LIVLGTSSSESALP M+ KME +G KSVVGLVIPTGYSFNLDG Sbjct: 248 YNFSLWAYLKYIRQEILIVLGTSSSESALPSMMQKMEAIGCDKSVVGLVIPTGYSFNLDG 307 Query: 307 TSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366 T+IYL MA +F+ Q + + QIT+L VL+++SKGAAGVTGSGFIVL +TL+A+ + Sbjct: 308 TAIYLAMAVIFLCQVFHVDLTLGQQITVLGVLMITSKGAAGVTGSGFIVLVSTLTALKIM 367 Query: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQ 411 P+ +++++G+DRFMSEARA+TN++GN VAT+V+AK K+ DE + Sbjct: 368 PIEHISILIGVDRFMSEARAITNVIGNGVATIVIAKSEKQFDEQK 412 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: 589 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: 428 Length adjustment: 32 Effective length of query: 412 Effective length of database: 396 Effective search space: 163152 Effective search space used: 163152 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