Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate AZOBR_RS21140 AZOBR_RS21140 C4-dicarboxylate ABC transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__azobra:AZOBR_RS21140 Length = 433 Score = 501 bits (1291), Expect = e-146 Identities = 248/412 (60%), Positives = 320/412 (77%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 ++P Y +L QV+ AI IGILLGHFYP V +KPLGD FIK+IKMVI PI+F TVV+GI Sbjct: 9 KKPFYTNLTVQVLTAITIGILLGHFYPALAVQMKPLGDVFIKMIKMVIGPIVFLTVVTGI 68 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 + + +MK VGK GG A+LYFEIV+T AL +GL+VVN+V+PG+GM+I +L A VA Y Sbjct: 69 SSIGDMKKVGKVGGKAILYFEIVTTFALGLGLLVVNLVKPGSGMNIQAGSLKADAVAKYA 128 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 T ++ + + F++N++P+ ++GAF GD+LQ+L F+VIFG AL +G GK V D ++ Sbjct: 129 TEAQNHTTIDFLVNIVPDNVIGAFVKGDMLQILFFAVIFGVALSAMGQKGKVVEDMFEKV 188 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 +H +F +I ++M++AP+GA GAM+FTIG YGV SL LGQLM YIT LFV VVLG+I Sbjct: 189 SHALFGVIGILMRVAPLGAFGAMSFTIGKYGVSSLTSLGQLMAAVYITMALFVFVVLGSI 248 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 R + FS+L +RYI++ELLIVLGTSSSES LPRM+ KM++ G K VVGLVIPTGYSFN Sbjct: 249 ARLYNFSLLTFLRYIKDELLIVLGTSSSESVLPRMMEKMQKFGCSKHVVGLVIPTGYSFN 308 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 LDGTSIYL+MAA+FIAQA + + I Q+T+L +L+L+SKGAA VTG GF+ LAATLSA Sbjct: 309 LDGTSIYLSMAAIFIAQAFNIDLTIWQQLTILGLLMLTSKGAAAVTGGGFVTLAATLSAT 368 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAE 415 GHLP+ GLAL+LG+DRFMSEARA+TNL+GN VAT+VVAK E DE + AE Sbjct: 369 GHLPIEGLALLLGVDRFMSEARAITNLIGNGVATIVVAKMEGEFDESKAVAE 420 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: 576 Number of extensions: 23 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: 444 Length of database: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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