Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate BWI76_RS02105 BWI76_RS02105 glutamate/aspartate:proton symporter GltP
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Koxy:BWI76_RS02105 Length = 437 Score = 330 bits (847), Expect = 4e-95 Identities = 174/419 (41%), Positives = 272/419 (64%), Gaps = 17/419 (4%) Query: 10 SLYFQVIVAIAIGILLG---HFYPQT-----GVALKPLGDGFIKLIKMVIAPIIFCTVVS 61 S+ +Q+++A+ +GILLG H++ ++ L P GD FI LIKM++ PI+ T+V Sbjct: 8 SMAWQILLALVLGILLGSYLHYHAESRDWLISNLLTPAGDIFIHLIKMIVVPIVISTLVV 67 Query: 62 GIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAA 121 GIAG+ + K +G+ G ++YFE+++T+A+++G+ + NV QPG+G ID+S L A ++ Sbjct: 68 GIAGVGDAKQLGRIGAKTIIYFEVITTVAIVLGITLANVFQPGSG--IDMSQLAAVDISK 125 Query: 122 YV-TAGKDQS----IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGA-YGKP 175 Y T + QS ++G IL+++P IV + A GD+L ++ FSV+FG L L A + +P Sbjct: 126 YQNTTAEVQSHAHGLMGTILSLVPTNIVASMAKGDMLPIIFFSVLFGLGLSSLPATHREP 185 Query: 176 VLDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLF 235 ++ + MF + +M+M+ AP+G ++ T+ +G SL L +L+I Y + F Sbjct: 186 LVTVFRSISETMFKVTHMVMRYAPVGVFALISVTVATFGFASLWPLAKLVILVYFAILFF 245 Query: 236 VLVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLV 295 LVVLG + R G S+ LIR +++EL++ T+SSES LPR++ KME GA S+ V Sbjct: 246 ALVVLGIVARVCGLSIWTLIRILKDELILAYSTASSESVLPRIIEKMEAYGAPASITSFV 305 Query: 296 IPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIV 355 +PTGYSFNLDG+++Y ++AA+FIAQ + I +ITL+L L+++SKG AGV G F+V Sbjct: 306 VPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEITLVLTLMVTSKGIAGVPGVSFVV 365 Query: 356 LAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQA 414 L ATL +VG +P+ GLA I G+DR + AR N+VGNA+A +V+AKW + D + A Sbjct: 366 LLATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKALA 423 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: 485 Number of extensions: 26 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