Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate PP_0137 PP_0137 glutamate/aspartate-proton DAACS transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Putida:PP_0137 Length = 442 Score = 321 bits (823), Expect = 3e-92 Identities = 173/407 (42%), Positives = 262/407 (64%), Gaps = 16/407 (3%) Query: 10 SLYFQVIVA----IAIGILLGHFYPQTGV----ALKPLGDGFIKLIKMVIAPIIFCTVVS 61 SL +Q+++ +AIG LL HF + L+P GD FI+LIKM++ PI+ +++ Sbjct: 7 SLAWQIVIGLVLGVAIGALLNHFSAEKAWWISNVLQPAGDIFIRLIKMIVVPIVISSLIV 66 Query: 62 GIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAA 121 GIAG+ + K +G G ++YFE+V+TIA+++GLV+ N+ PG G ID+STL ++ Sbjct: 67 GIAGVGDAKKLGSIGLKTIIYFEVVTTIAIVVGLVLANLFHPGAG--IDMSTLGTVDISK 124 Query: 122 Y-VTAGKDQSIVGFI---LNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGK-PV 176 Y TA + Q FI LN+IP+ I A G++L ++ FSV+FG L L A + P+ Sbjct: 125 YQATAAEVQHEHAFIETLLNLIPSNIFAALMRGEMLPIIFFSVMFGLGLSSLQAELRDPL 184 Query: 177 LDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFV 236 + + MF + +MIM APIG +A T+ +G SL+ L +L++ Y F Sbjct: 185 VRTFQAVSETMFKVTHMIMNYAPIGVFALIAVTVANFGFSSLLPLAKLVVLVYFAIAFFA 244 Query: 237 LVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVI 296 +VLG + R GFSV+K++R +++EL++ TSSSE+ LPR++ KME+ GA KS+ V+ Sbjct: 245 FMVLGLVARLFGFSVIKIMRIMKDELILAYSTSSSETVLPRVIEKMEKYGAPKSICSFVV 304 Query: 297 PTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVL 356 PTGYSFNLDG+++Y ++AA+FIAQ + + Q+ L+L L+++SKG AGV G F+VL Sbjct: 305 PTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSWSQQLLLVLTLMVTSKGIAGVPGVSFVVL 364 Query: 357 AATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKW 403 ATL +VG +P+ GLA I G+DR M AR N+VGNA+A +V+A+W Sbjct: 365 LATLGSVG-IPLEGLAFIAGVDRIMDMARTALNVVGNALAALVIARW 410 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: 500 Number of extensions: 23 Number of successful extensions: 6 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: 442 Length adjustment: 32 Effective length of query: 412 Effective length of database: 410 Effective search space: 168920 Effective search space used: 168920 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