Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 18105 b4077 glutamate/aspartate:proton symporter (NCBI)
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Keio:18105 Length = 437 Score = 323 bits (827), Expect = 9e-93 Identities = 171/417 (41%), Positives = 268/417 (64%), Gaps = 13/417 (3%) Query: 10 SLYFQVIVAIAIGILLG---HFYPQTGV-----ALKPLGDGFIKLIKMVIAPIIFCTVVS 61 SL +Q++ A+ +GILLG H++ + L P GD FI LIKM++ PI+ T+V Sbjct: 7 SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVV 66 Query: 62 GIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHID-VSTLDASKVA 120 GIAG+ + K +G+ G ++YFE+++T+A+++G+ + NV QPG G+ + ++T+D SK Sbjct: 67 GIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKYQ 126 Query: 121 AYVTAGKDQS--IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGA-YGKPVL 177 + A + S I+G IL+++P IV + A G++L ++ FSV+FG L L A + +P++ Sbjct: 127 STTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREPLV 186 Query: 178 DFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVL 237 + MF + +M+M+ AP+G +A T+ +G SL L +L++ + + F L Sbjct: 187 TVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFFAL 246 Query: 238 VVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIP 297 VVLG + R G SV LIR +++EL++ T+SSES LPR++ KME GA S+ V+P Sbjct: 247 VVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFVVP 306 Query: 298 TGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLA 357 TGYSFNLDG+++Y ++AA+FIAQ + I +I L+L L+++SKG AGV G F+VL Sbjct: 307 TGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVVLL 366 Query: 358 ATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQA 414 ATL +VG +P+ GLA I G+DR + AR N+VGNA+A +V+AKW + D + A Sbjct: 367 ATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKALA 422 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: 495 Number of extensions: 23 Number of successful extensions: 5 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: 437 Length adjustment: 32 Effective length of query: 412 Effective length of database: 405 Effective search space: 166860 Effective search space used: 166860 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